Mercurial > repos > saskia-hiltemann > annovar
annotate tools/annovar/annovar.sh @ 5:4600be69b96f draft
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
author | saskia-hiltemann |
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date | Thu, 01 Oct 2015 04:24:45 -0400 |
parents | ff5325029a8e |
children | 69e2067a120d |
rev | line source |
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0 | 1 #!/bin/bash |
2 | |
3 test="N" | |
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4 dofilter="N" |
0 | 5 |
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6 ######################### |
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7 # DEFINE SOME |
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8 # FUNCTIONS |
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9 ######################### |
0 | 10 |
11 function usage(){ | |
12 echo "usage: $0 todo" | |
13 } | |
14 | |
15 function runfilter(){ | |
16 ifile=$1 | |
17 columnname=$2 | |
18 threshold=$3 | |
19 | |
20 if [[ $threshold == "-1" ]] | |
21 then | |
22 echo "not filtering" | |
23 return | |
24 fi | |
25 | |
26 echo "filtering: $columnname, $threshold" | |
27 cat $ifile | |
28 | |
29 #get column number corresponding to column header | |
30 column=`awk 'BEGIN{ | |
31 FS="\t"; | |
32 col=-1 | |
33 }{ | |
34 if(FNR==1){ | |
35 for(i=1;i<=NF;i++){ | |
36 if($i == "'"${columnname}"'") | |
37 col=i | |
38 } | |
39 print col | |
40 } | |
41 }' $ifile ` | |
42 | |
43 if [ $column == -1 ] | |
44 then | |
45 echo "no such column, exiting" | |
46 return | |
47 fi | |
48 | |
49 #perform filtering using the threshold | |
50 awk 'BEGIN{ | |
51 FS="\t"; | |
52 OFS="\t"; | |
53 }{ | |
54 if(FNR==1) | |
55 print $0; | |
56 if(FNR>1){ | |
57 if( $"'"${column}"'" == "" ) # empty column, then print | |
58 print $0 | |
59 else if ("'"${threshold}"'" == "text"){} #if set to text dont check threshold | |
60 | |
61 else if ($"'"${column}"'" < "'"${threshold}"'") #else do check it | |
62 print $0 | |
63 } | |
64 }' $ifile > tmpfile | |
65 | |
66 mv tmpfile $ifile | |
67 } | |
68 | |
69 # arguments: originalfile,resultfile,chrcol,startcol,endcol,refcol,obscol,addcols | |
70 function joinresults(){ | |
71 ofile=$1 | |
72 rfile=$2 | |
73 colchr=$3 | |
74 colstart=$4 | |
75 colend=$5 | |
76 colref=$6 | |
77 colobs=$7 | |
78 addcols=$8 #e.g. "B.col1,B.col2" | |
79 | |
80 test="N" | |
81 | |
82 # echo "joining result with original file" | |
83 if [ $test == "Y" ] | |
84 then | |
85 echo "ofile: $ofile" | |
86 head $ofile | |
87 echo "rfile: $rfile" | |
88 head $rfile | |
89 fi | |
90 numlines=`wc $rfile | cut -d" " -f2` | |
91 | |
92 # if empty results file, just add header fields | |
93 if [[ ! -s $rfile ]] | |
94 then | |
95 dummycol=${addcols:2} | |
96 outputcol=${dummycol//",B."/" "} | |
97 numcommas=`echo "$addcols" | grep -o "," | wc -l` | |
98 | |
99 awk 'BEGIN{FS="\t";OFS="\t"}{ | |
100 if(FNR==1) | |
101 print $0,"'"$outputcol"'"; | |
102 else{ | |
103 printf $0 | |
104 for(i=0;i<="'"$numcommas"'"+1;i++) | |
105 printf "\t" | |
106 printf "\n" | |
107 } | |
108 }END{}' $ofile > tempofile | |
109 | |
110 mv tempofile $ofile | |
111 return | |
112 fi | |
113 | |
114 | |
115 #get input file column names for cgatools join | |
116 col_chr_name=`head -1 $rfile | cut -f${colchr}` | |
117 col_start_name=`head -1 $rfile | cut -f${colstart}` | |
118 col_end_name=`head -1 $rfile | cut -f${colend}` | |
119 col_ref_name=`head -1 $rfile | cut -f${colref}` | |
120 col_obs_name=`head -1 $rfile | cut -f${colobs}` | |
121 | |
122 #get annotation file column names for cgatools join | |
123 chr_name=`head -1 $ofile | cut -f${chrcol}` | |
124 start_name=`head -1 $ofile | cut -f${startcol}` | |
125 end_name=`head -1 $ofile | cut -f${endcol}` | |
126 ref_name=`head -1 $ofile | cut -f${refcol}` | |
127 obs_name=`head -1 $ofile | cut -f${obscol}` | |
128 | |
129 if [ $test == "Y" ] | |
130 then | |
131 echo "input file" | |
132 echo "chr col: $col_chr_name ($colchr)" | |
133 echo "start col: $col_start_name ($colstart)" | |
134 echo "end col: $col_end_name ($colend)" | |
135 echo "ref col: $col_ref_name ($colref)" | |
136 echo "obs col: $col_obs_name ($colobs)" | |
137 echo "" | |
138 echo "annotation file" | |
139 echo "chr col: $chr_name ($chrcol)" | |
140 echo "start col: $start_name ($startcol)" | |
141 echo "end col: $end_name ($endcol)" | |
142 echo "ref col: $ref_name ($refcol)" | |
143 echo "obs col: $obs_name ($obscol)" | |
144 fi | |
145 | |
146 #perform join | |
147 cgatools join --beta \ | |
148 --input $ofile $rfile \ | |
149 --output temporiginal \ | |
150 --match ${chr_name}:${col_chr_name} \ | |
151 --match ${start_name}:${col_start_name} \ | |
152 --match ${end_name}:${col_end_name} \ | |
153 --match ${ref_name}:${col_ref_name} \ | |
154 --match ${obs_name}:${col_obs_name} \ | |
155 --select A.*,$addcols \ | |
156 --always-dump \ | |
157 --output-mode compact | |
158 | |
159 #replace originalfile | |
160 sed -i 's/^>//g' temporiginal #join sometimes adds a '>' symbol to header | |
161 mv temporiginal originalfile | |
162 | |
163 if [ $test == "Y" ] | |
164 then | |
165 echo "joining complete" | |
166 head originalfile | |
167 echo "" | |
168 fi | |
169 | |
170 } | |
171 | |
172 | |
173 | |
174 | |
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175 ################################# |
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176 # |
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177 # PARSE PARAMETERS |
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178 # |
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179 ################################# |
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180 |
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181 |
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182 set -- `getopt -n$0 -u -a --longoptions="inputfile: buildver: humandb: varfile: VCF: chrcol: startcol: endcol: refcol: obscol: vartypecol: convertcoords: geneanno: hgvs: verdbsnp: tfbs: mce: cytoband: segdup: dgv: gwas: ver1000g: cg46: cg69: impactscores: newimpactscores: otherinfo: esp: exac03: spidex: gonl: gerp: cosmic61: cosmic63: cosmic64: cosmic65: cosmic67: cosmic68: clinvar: nci60: outall: outfilt: outinvalid: scriptsdir: dorunannovar: dofilter: filt_dbsnp: filt1000GALL: filt1000GAFR: filt1000GAMR: filt1000GASN: filt1000GEUR: filtESP6500ALL: filtESP6500EA: filtESP6500AA: filtcg46: filtcg69: dummy:" "h:" "$@"` || usage |
0 | 183 [ $# -eq 0 ] && usage |
184 | |
185 | |
186 | |
187 while [ $# -gt 0 ] | |
188 do | |
189 case "$1" in | |
190 --inputfile) infile=$2;shift;; # inputfile | |
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191 --buildver) buildvertmp=$2;shift;; # hg18 or hg19 |
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192 --humandb) humandbtmp=$2;shift;; # location of humandb database |
0 | 193 --varfile) varfile=$2;shift;; # Y or N |
194 --VCF) vcf=$2;shift;; #Y or N | |
195 --chrcol) chrcol=$2;shift;; # which column has chr | |
196 --startcol) startcol=$2;shift;; # which column has start | |
197 --endcol) endcol=$2;shift;; # which column has end | |
198 --refcol) refcol=$2;shift;; # which column has ref | |
199 --obscol) obscol=$2;shift;; # which column has alt | |
200 --vartypecol) vartypecol=$2;shift;; # which column has vartype | |
201 --convertcoords) convertcoords=$2;shift;; # Y or N convert coordinate from CG to 1-based? | |
202 --geneanno) geneanno=$2;shift;; # comma-separated list of strings refSeq, knowngene, ensgene | |
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203 --hgvs) hgvs=$2;shift;; |
3 | 204 --verdbsnp) verdbsnp=$2;shift;; #comma-separated list of dbsnp version to annotate with (e.g. "132,135NonFlagged,137,138")" |
0 | 205 --tfbs) tfbs=$2;shift;; # Y or N |
206 --mce) mce=$2;shift;; # Y or N | |
207 --cytoband) cytoband=$2;shift;; # Y or N | |
208 --segdup) segdup=$2;shift;; # Y or N | |
209 --dgv) dgv=$2;shift;; # Y or N | |
210 --gwas) gwas=$2;shift;; # Y or N | |
211 --ver1000g) ver1000g=$2;shift;; # Y or N | |
212 --cg46) cg46=$2;shift;; | |
213 --cg69) cg69=$2;shift;; | |
214 --impactscores) impactscores=$2;shift;; # Y or N | |
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215 --newimpactscores) newimpactscores=$2;shift;; # Y or N |
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216 --otherinfo) otherinfo=$2;shift;; |
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217 --scriptsdir) scriptsdirtmp=$2;shift;; # Y or N |
0 | 218 --esp) esp=$2;shift;; # Y or N |
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219 --exac03) exac03=$2;shift;; |
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220 --gonl) gonl=$2;shift;; |
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221 --spidex) spidex=$2;shift;; |
0 | 222 --gerp) gerp=$2;shift;; # Y or N |
223 --cosmic61) cosmic61=$2;shift;; # Y or N | |
224 --cosmic63) cosmic63=$2;shift;; # Y or N | |
225 --cosmic64) cosmic64=$2;shift;; # Y or N | |
226 --cosmic65) cosmic65=$2;shift;; # Y or N | |
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227 --cosmic67) cosmic67=$2;shift;; # Y or N |
3 | 228 --cosmic68) cosmic68=$2;shift;; # Y or N |
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229 --nci60) nci60=$2;shift;; # Y or N |
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230 --clinvar) clinvar=$2;shift;; # Y or N |
0 | 231 --filt_dbsnp) filt_dbsnp=$2;shift;; |
232 --filt1000GALL) threshold_1000g_ALL=$2;shift;; #threshold value | |
233 --filt1000GAFR) threshold_1000g_AFR=$2;shift;; #threshold value | |
234 --filt1000GAMR) threshold_1000g_AMR=$2;shift;; #threshold value | |
235 --filt1000GASN) threshold_1000g_ASN=$2;shift;; #threshold value | |
236 --filt1000GEUR) threshold_1000g_EUR=$2;shift;; #threshold value | |
237 --filtESP6500ALL) threshold_ESP6500_ALL=$2;shift;; #threshold value | |
238 --filtESP6500EA) threshold_ESP6500_EA=$2;shift;; #threshold value | |
239 --filtESP6500AA) threshold_ESP6500_AA=$2;shift;; #threshold value | |
240 --filtcg46) threshold_cg46=$2;shift;; | |
241 --filtcg69) threshold_cg69=$2;shift;; | |
242 --outall) outfile_all=$2;shift;; # file | |
243 --outfilt) outfile_filt=$2;shift;; # file | |
244 --outinvalid) outfile_invalid=$2;shift;; #file | |
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245 --dorunannovar) dorunannovar=$2;shift;; #Y or N |
0 | 246 -h) shift;; |
247 --) shift;break;; | |
248 -*) usage;; | |
249 *) break;; | |
250 esac | |
251 shift | |
252 done | |
253 | |
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254 #sometimes galaxy screws up these variables after updates, if comma-separated list, use only what is before first comma |
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255 humandb=${humandbtmp%,*} |
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256 buildver=${buildvertmp%,*} |
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257 scriptsdir=${scriptsdirtmp%,*} |
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258 |
0 | 259 |
260 if [ $test == "Y" ] | |
261 then | |
262 echo "dorunannovar: $dorunannovar" | |
263 echo "infile: $infile" | |
264 echo "buildver: $buildver" | |
265 echo "annovardb: $humandb" | |
266 echo "verdbnsp: $verdbsnp" | |
267 echo "geneanno: $geneanno" | |
268 echo "tfbs: $tfbs" | |
269 echo "mce: $mce" | |
270 echo "cytoband: $cytoband" | |
271 echo "segdup: $segdup" | |
272 echo "dgv: $dgv" | |
273 echo "gwas: $gwas" | |
274 echo "g1000: ${g1000}" | |
275 echo "cg46: ${cg46}" | |
276 echo "cg69: ${cg69}" | |
277 echo "impactscores: $impactscores" | |
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278 echo "impactscores: $newimpactscores" |
0 | 279 echo "esp: $esp" |
280 echo "gerp: $gerp" | |
281 echo "cosmic: $cosmic" | |
282 echo "outfile: $outfile_all" | |
283 echo "outinvalid: $outfile_invalid" | |
284 echo "outfiltered: $outfile_filt" | |
285 echo "varfile: $varfile" | |
286 echo "vcf" $vcf | |
287 echo "chrcol: $chrcol" | |
288 echo "startcol: $startcol" | |
289 echo "endcol: $endcol" | |
290 echo "refcol: $refcol" | |
291 echo "obscol: $obscol" | |
292 echo "convertcoords: $convertcoords" | |
293 echo "vartypecol: $vartypecol" | |
294 echo "dofilter: $dofilter" | |
295 echo "threshold_1000g_ALL : $threshold_1000g_ALL" | |
296 echo "threshold_1000g_AFR : $threshold_1000g_AFR" | |
297 echo "threshold_1000g_AMR : $threshold_1000g_AMR" | |
298 echo "threshold_1000g_ASN : $threshold_1000g_ASN" | |
299 echo "threshold_1000g_EUR : $threshold_1000g_EUR" | |
300 echo "threshold_ESP6500_ALL: $threshold_ESP6500_ALL" | |
301 echo "threshold_ESP6500_EA : $threshold_ESP6500_EA" | |
302 echo "threshold_ESP6500_AA : $threshold_ESP6500_AA" | |
303 | |
304 fi | |
305 | |
306 | |
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307 |
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308 ############################################ |
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309 # |
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310 # Annotate Variants |
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311 # |
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312 ############################################ |
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313 |
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314 #parse geneanno param |
0 | 315 refgene="N" |
316 knowngene="N" | |
317 ensgene="N" | |
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318 |
0 | 319 if [[ $geneanno =~ "refSeq" ]] |
320 then | |
321 refgene="Y" | |
322 fi | |
323 if [[ $geneanno =~ "knowngene" ]] | |
324 then | |
325 knowngene="Y" | |
326 fi | |
327 if [[ $geneanno =~ "ensgene" ]] | |
328 then | |
329 ensgene="Y" | |
330 fi | |
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331 if [ $hgvs == "N" ] |
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332 then |
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333 hgvs="" |
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334 fi |
0 | 335 |
336 #parse verdbsnp/1000g/esp strings | |
337 dbsnpstr=${verdbsnp//,/ } | |
338 filt_dbsnpstr=${filt_dbsnp//,/ } | |
339 g1000str=${ver1000g//,/ } | |
340 espstr=${esp//,/ } | |
341 | |
342 if [ $test == "Y" ] | |
343 then | |
344 echo "annotate dbsnp: $dbsnpstr" | |
345 echo "annotate esp: $espstr" | |
346 echo "filter dbsnp: $filt_dbsnpstr" | |
347 fi | |
348 | |
349 mutationtaster="N" | |
350 avsift="N" | |
351 lrt="N" | |
352 polyphen2="N" | |
353 phylop="N" | |
354 ljbsift="N" | |
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355 |
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356 #parse old impactscores param (obsolete) |
0 | 357 if [[ $impactscores =~ "mutationtaster" ]] |
358 then | |
359 mutationtaster="Y" | |
360 fi | |
361 if [[ $impactscores =~ "sift" ]] | |
362 then | |
363 avsift="Y" | |
364 fi | |
365 if [[ $impactscores =~ "lrt" ]] | |
366 then | |
367 lrt="Y" | |
368 fi | |
369 if [[ $impactscores =~ "ljbsift" ]] | |
370 then | |
371 ljbsift="Y" | |
372 fi | |
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373 if [[ $impactscores =~ "ljb2sift" ]] |
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374 then |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
375 ljb2sift="Y" |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
376 fi |
0 | 377 if [[ $impactscores =~ "pp2" ]] |
378 then | |
379 polyphen2="Y" | |
380 fi | |
381 if [[ $impactscores =~ "phylop" ]] | |
382 then | |
383 phylop="Y" | |
384 fi | |
385 | |
386 if [[ $varfile == "Y" ]] | |
387 then | |
388 convertcoords="Y" | |
389 fi | |
390 | |
391 #ljb refers to Liu, Jian, Boerwinkle paper in Human Mutation with pubmed ID 21520341. Cite this paper if you use the scores | |
392 | |
2
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
393 ljb2_sift="N" |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
394 ljb2_pp2hdiv="N" |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
395 ljb2_pp2hvar="N" |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
396 ljb2_lrt="N" |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
397 ljb2_mt="N" |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
398 ljb2_ma="N" |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
399 ljb2_fathmm="N" |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
400 ljb2_gerp="N" |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
401 ljb2_phylop="N" |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
402 ljb2_siphy="N" |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
403 |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
404 # parse ljb2 newimpactscores param |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
405 # ljb2_sift, ljb2_pp2hdiv, ljb2_pp2hvar, ljb2_lrt, ljb2_mt, ljb2_ma, ljb2_fathmm, ljb2_gerp++, ljb2_phylop, ljb2_siphy |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
406 if [[ $newimpactscores =~ "ljb2_sift" ]] |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
407 then |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
408 ljb2_sift="Y" |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
409 fi |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
410 if [[ $newimpactscores =~ "ljb2_pp2hdiv" ]] |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
411 then |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
412 ljb2_pp2hdiv="Y" |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
413 fi |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
414 if [[ $newimpactscores =~ "ljb2_pp2hvar" ]] |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
415 then |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
416 ljb2_pp2hvar="Y" |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
417 fi |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
418 if [[ $newimpactscores =~ "ljb2_lrt" ]] |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
419 then |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
420 ljb2_lrt="Y" |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
421 fi |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
422 if [[ $newimpactscores =~ "ljb2_mt" ]] |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
423 then |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
424 ljb2_mt="Y" |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
425 fi |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
426 if [[ $newimpactscores =~ "ljb2_ma" ]] |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
427 then |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
428 ljb2_ma="Y" |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
429 fi |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
430 if [[ $newimpactscores =~ "ljb2_fathmm" ]] |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
431 then |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
432 ljb2_fathmm="Y" |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
433 fi |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
434 if [[ $newimpactscores =~ "ljb2_gerp" ]] |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
435 then |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
436 ljb2_gerp="Y" |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
437 fi |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
438 if [[ $newimpactscores =~ "ljb2_phylop" ]] |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
439 then |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
440 ljb2_phylop="Y" |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
441 fi |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
442 if [[ $newimpactscores =~ "ljb2_siphy" ]] |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
443 then |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
444 ljb2_siphy="Y" |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
445 fi |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
446 |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
447 if [ $otherinfo == "N" ] |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
448 then |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
449 otherinfo="" |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
450 fi |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
451 |
0 | 452 |
453 #column header names we will be adding | |
454 # ESP 6500 | |
455 esp6500si_colheader_ALL="ESP6500si_ALL" | |
456 esp6500si_colheader_EA="ESP6500si_EA" | |
457 esp6500si_colheader_AA="ESP6500si_AA" | |
458 esp6500_colheader_ALL="ESP6500_ALL" | |
459 esp6500_colheader_EA="ESP6500_EA" | |
460 esp6500_colheader_AA="ESP6500_AA" | |
461 esp5400si_colheader_ALL="ESP5400si_ALL" | |
462 esp5400si_colheader_EA="ESP5400si_EA" | |
463 esp5400si_colheader_AA="ESP5400si_AA" | |
464 esp5400_colheader_ALL="ESP5400_ALL" | |
465 esp5400_colheader_EA="ESP5400_EA" | |
466 esp5400_colheader_AA="ESP5400_AA" | |
467 | |
468 | |
469 # cg46 cg69 | |
470 cg46_colheader="CG_46_genomes" | |
471 cg69_colheader="CG_69_genomes" | |
472 | |
473 cp $infile originalfile | |
474 #run annovar or filter only? | |
475 if [ $dorunannovar == "Y" ] | |
476 then | |
477 | |
478 | |
479 #################################### | |
480 # | |
481 # PREPARE INPUT FILE | |
482 # | |
483 #################################### | |
484 | |
485 echo "converting input file" | |
486 vcfheader="" | |
487 if [ $vcf == "Y" ] #if CG varfile, convert | |
488 then | |
489 # convert vcf to annovarinput | |
3 | 490 $scriptsdir/convert2annovar.pl --format vcf4old --allallele --includeinfo --outfile annovarinput $infile 2>&1 |
0 | 491 |
492 #construct header line from vcf file | |
493 cat $infile | grep "#CHROM" > additionalcols | |
494 sed -i 's/#//g' additionalcols | |
495 vcfheader="\t`cat additionalcols`" | |
496 echo "vcfheader:$vcfheader" | |
497 echo -e "chromosome\tbegin\tend\treference\tobserved\t`cat additionalcols`" > originalfile | |
498 cat annovarinput >> originalfile | |
499 | |
500 chrcol=1 | |
501 startcol=2 | |
502 endcol=3 | |
503 refcol=4 | |
504 obscol=5 | |
505 | |
506 | |
507 elif [ $varfile == "Y" ] #if CG varfile, convert | |
508 then | |
509 # convert varfile | |
510 $scriptsdir/convert2annovar.pl --format cg --outfile annovarinput $infile 2>&1 | |
511 echo -e "chromosome\tbegin\tend\treference\talleleSeq\tvarType\thaplotype" > originalfile | |
512 cat annovarinput | cut -f1-6,8 >> originalfile | |
513 cat annovarinput | cut -f1-5 >> annovarinput2 | |
514 mv annovarinput2 annovarinput | |
515 | |
516 chrcol=1 | |
517 startcol=2 | |
518 endcol=3 | |
519 refcol=4 | |
520 obscol=5 | |
521 | |
522 elif [ $convertcoords == "Y" ] # if CG-coordinates, convert | |
523 then | |
524 #echo "rearranging columns and converting coordinates" | |
525 awk 'BEGIN{ | |
526 FS="\t"; | |
527 OFS="\t"; | |
528 }{ | |
529 if(FNR>1) { | |
5
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
530 gsub(/chr/,"",$"'"${chrcol}"'") |
0 | 531 if( $"'"${vartypecol}"'" == "snp" ){ $"'"${startcol}"'" += 1 }; |
532 if( $"'"${vartypecol}"'" == "ins" ){ $"'"${refcol}"'" = "-" }; | |
533 if( $"'"${vartypecol}"'" == "del" ){ $"'"${startcol}"'" +=1; $"'"${obscol}"'" = "-" }; | |
534 if( $"'"${vartypecol}"'" == "sub" ){ $"'"${startcol}"'" += 1 }; | |
535 | |
536 printf("%s\t%s\t%s\t%s\t%s\n" ,$"'"${chrcol}"'",$"'"${startcol}"'",$"'"${endcol}"'",$"'"${refcol}"'",$"'"${obscol}"'"); | |
537 } | |
538 } | |
539 END{ | |
540 }' $infile > annovarinput | |
541 | |
542 #remove any "chr" prefixes | |
5
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
543 #sed -i '2,$s/chr//g' annovarinput |
0 | 544 |
545 awk 'BEGIN{ | |
546 FS="\t"; | |
5
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
547 OFS="\t"; |
0 | 548 }{ |
5
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
549 |
0 | 550 if(FNR>=1) { |
5
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
551 gsub(/chr/,"",$"'"${chrcol}"'") |
0 | 552 if( $"'"${vartypecol}"'" == "snp" ){ $"'"${startcol}"'" += 1 }; |
553 if( $"'"${vartypecol}"'" == "ins" ){ $"'"${refcol}"'" = "-" }; | |
554 if( $"'"${vartypecol}"'" == "del" ){ $"'"${startcol}"'" +=1; $"'"${obscol}"'" = "-" }; | |
555 if( $"'"${vartypecol}"'" == "sub" ){ $"'"${startcol}"'" += 1 }; | |
556 | |
557 print $0 | |
558 } | |
559 } | |
560 END{ | |
561 }' $infile > originalfile | |
562 | |
563 #remove any "chr" prefixes | |
5
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
564 #sed -i '2,$s/chr//g' originalfile |
0 | 565 sed -i 's/omosome/chromosome/g' originalfile |
566 | |
567 | |
568 else #only rearrange columns if already 1-based coordinates | |
569 echo "rearranging columns " | |
570 awk 'BEGIN{ | |
571 FS="\t"; | |
572 OFS="\t"; | |
573 }{ | |
5
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
574 if(FNR>1) { |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
575 printf("%s\t%s\t%s\t%s\t%s\n",$"'"${chrcol}"'",$"'"${startcol}"'",$"'"${endcol}"'",$"'"${refcol}"'",$"'"${obscol}"'"); |
0 | 576 } |
577 } | |
578 END{ | |
579 }' $infile > annovarinput | |
580 | |
581 #remove any "chr" prefixes | |
5
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
582 sed -i '2,$s/chr//g' annovarinput |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
583 sed '2,$s/chr//g' $infile > originalfile |
0 | 584 sed -i 's/omosome/chromosome/g' originalfile |
585 fi | |
586 | |
587 echo "...finished conversion" | |
588 | |
589 | |
590 | |
591 | |
592 #################################### | |
593 # | |
594 # RUN ANNOVAR COMMANDS | |
595 # | |
596 #################################### | |
597 | |
598 | |
599 | |
600 ###### gene-based annotation ####### | |
601 | |
602 # RefSeq Gene | |
603 if [ $refgene == "Y" ] | |
604 then | |
605 echo -e "\nrefSeq gene" | |
2
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
606 $scriptsdir/annotate_variation.pl --geneanno --buildver $buildver -dbtype gene ${hgvs} annovarinput $humandb 2>&1 |
0 | 607 |
608 annovarout=annovarinput.variant_function | |
609 sed -i '1i\RefSeq_Func\tRefSeq_Gene\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout | |
610 joinresults originalfile $annovarout 3 4 5 6 7 B.RefSeq_Func,B.RefSeq_Gene | |
611 | |
612 annovarout=annovarinput.exonic_variant_function | |
613 sed -i '1i\linenum\tRefSeq_ExonicFunc\tRefSeq_AAChange\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout | |
614 joinresults originalfile $annovarout 4 5 6 7 8 B.RefSeq_ExonicFunc,B.RefSeq_AAChange | |
615 fi | |
616 | |
617 | |
618 # UCSC KnownGene | |
619 if [ $knowngene == "Y" ] | |
620 then | |
621 echo -e "\nUCSC known gene" | |
622 $scriptsdir/annotate_variation.pl --geneanno --buildver $buildver -dbtype knowngene annovarinput $humandb 2>&1 | |
623 | |
624 annovarout=annovarinput.variant_function | |
625 sed -i '1i\UCSCKnownGene_Func\tUCSCKnownGene_Gene\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout | |
626 joinresults originalfile $annovarout 3 4 5 6 7 B.UCSCKnownGene_Func,B.UCSCKnownGene_Gene | |
627 | |
628 annovarout=annovarinput.exonic_variant_function | |
629 sed -i '1i\linenum\tUCSCKnownGene_ExonicFunc\tUCSCKnownGene_AAChange\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout | |
630 joinresults originalfile $annovarout 4 5 6 7 8 B.UCSCKnownGene_ExonicFunc,B.UCSCKnownGene_AAChange | |
631 fi | |
632 | |
633 | |
634 # Emsembl Gene | |
635 if [ $ensgene == "Y" ] | |
636 then | |
637 echo -e "\nEnsembl gene" | |
638 $scriptsdir/annotate_variation.pl --geneanno --buildver $buildver -dbtype ensgene annovarinput $humandb 2>&1 | |
639 | |
640 annovarout=annovarinput.variant_function | |
641 sed -i '1i\EnsemblGene_Func\tEnsemblGene_Gene\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout | |
642 joinresults originalfile $annovarout 3 4 5 6 7 B.EnsemblGene_Func,B.EnsemblGene_Gene | |
643 | |
644 annovarout=annovarinput.exonic_variant_function | |
645 sed -i '1i\linenum\tEnsemblGene_ExonicFunc\tEnsemblGene_AAChange\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout | |
646 joinresults originalfile $annovarout 4 5 6 7 8 B.EnsemblGene_ExonicFunc,B.EnsemblGene_AAChange | |
647 fi | |
648 | |
649 | |
650 | |
651 ###### region-based annotation ####### | |
652 | |
653 | |
654 # Transcription Factor Binding Sites Annotation | |
655 if [ $mce == "Y" ] | |
656 then | |
657 echo -e "\nMost Conserved Elements" | |
658 | |
659 if [ $buildver == "hg18" ] | |
660 then | |
661 $scriptsdir/annotate_variation.pl --regionanno --buildver $buildver -dbtype mce44way annovarinput $humandb 2>&1 | |
662 annovarout=annovarinput.${buildver}_phastConsElements44way | |
663 sed -i '1i\db\tphastConsElements44way\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout | |
664 joinresults originalfile $annovarout 3 4 5 6 7 B.phastConsElements44way | |
665 | |
666 else #hg19 | |
667 $scriptsdir/annotate_variation.pl --regionanno --buildver $buildver -dbtype mce46way annovarinput $humandb 2>&1 | |
668 annovarout=annovarinput.${buildver}_phastConsElements46way | |
669 sed -i '1i\db\tphastConsElements46way\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout | |
670 joinresults originalfile $annovarout 3 4 5 6 7 B.phastConsElements46way | |
671 fi | |
672 | |
673 fi | |
674 | |
675 | |
676 | |
677 # Transcription Factor Binding Sites Annotation | |
678 if [ $tfbs == "Y" ] | |
679 then | |
680 echo -e "\nTranscription Factor Binding Site Annotation" | |
681 $scriptsdir/annotate_variation.pl --regionanno --buildver $buildver -dbtype tfbs annovarinput $humandb 2>&1 | |
682 | |
683 # arguments: originalfile, resultfile,chrcol,startcol,endcol,refcol,obscol,selectcolumns | |
684 annovarout=annovarinput.${buildver}_tfbsConsSites | |
685 sed -i '1i\db\tTFBS\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout | |
686 joinresults originalfile $annovarout 3 4 5 6 7 B.TFBS | |
687 fi | |
688 | |
689 | |
690 | |
691 # Identify cytogenetic band for genetic variants | |
692 if [ $cytoband == "Y" ] | |
693 then | |
694 echo -e "\nCytogenic band Annotation" | |
695 $scriptsdir/annotate_variation.pl --regionanno --buildver $buildver -dbtype band annovarinput $humandb 2>&1 | |
696 | |
697 annovarout=annovarinput.${buildver}_cytoBand | |
698 sed -i '1i\db\tBand\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout | |
699 joinresults originalfile $annovarout 3 4 5 6 7 B.Band | |
700 fi | |
701 | |
702 | |
703 # Identify variants located in segmental duplications | |
704 if [ $segdup == "Y" ] | |
705 then | |
706 echo -e "\nSegmental Duplications Annotation" | |
707 $scriptsdir/annotate_variation.pl --regionanno --buildver $buildver -dbtype segdup annovarinput $humandb 2>&1 | |
708 | |
709 annovarout=annovarinput.${buildver}_genomicSuperDups | |
710 sed -i '1i\db\tSegDup\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout | |
711 joinresults originalfile $annovarout 3 4 5 6 7 B.SegDup | |
712 fi | |
713 | |
714 | |
715 | |
716 # Identify previously reported structural variants in DGV | |
717 if [ $dgv == "Y" ] | |
718 then | |
719 echo -e "\nDGV Annotation" | |
2
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
720 $scriptsdir/annotate_variation.pl --regionanno --buildver $buildver -dbtype dgvMerged annovarinput $humandb 2>&1 |
0 | 721 |
2
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
722 annovarout=annovarinput.${buildver}_dgvMerged |
0 | 723 sed -i '1i\db\tDGV\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout |
724 joinresults originalfile $annovarout 3 4 5 6 7 B.DGV | |
725 fi | |
726 | |
727 | |
728 # Identify variants reported in previously published GWAS studies | |
729 if [ $gwas == "Y" ] | |
730 then | |
731 echo -e "\nGWAS Annotation" | |
732 $scriptsdir/annotate_variation.pl --regionanno --buildver $buildver -dbtype gwascatalog annovarinput $humandb 2>&1 | |
733 | |
734 annovarout=annovarinput.${buildver}_gwasCatalog | |
735 sed -i '1i\db\tGWAS\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout | |
736 joinresults originalfile $annovarout 3 4 5 6 7 B.GWAS | |
737 fi | |
738 | |
739 | |
740 | |
741 | |
742 ###### filter-based annotation ####### | |
743 | |
744 #dbSNP | |
745 for version in $dbsnpstr | |
746 do | |
747 if [ $version == "None" ] | |
748 then | |
749 break | |
750 fi | |
751 echo -e "\ndbSNP region Annotation, version: $version" | |
752 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype ${version} annovarinput $humandb 2>&1 | |
753 | |
5
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
754 columnname=${version} |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
755 if [[ $columnname == snp* ]] |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
756 then |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
757 columnname="db${version}" |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
758 fi |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
759 |
0 | 760 annovarout=annovarinput.${buildver}_${version}_dropped |
5
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
761 sed -i '1i\db\t'${columnname}'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
762 joinresults originalfile $annovarout 3 4 5 6 7 B.${columnname} |
0 | 763 |
764 | |
765 done | |
766 | |
767 | |
768 | |
769 #1000 Genomes | |
770 | |
771 if [ $ver1000g != "None" ] | |
772 then | |
773 | |
774 for version in $g1000str | |
775 do | |
776 #column headers | |
777 g1000_colheader_ALL="${version}_ALL" | |
778 g1000_colheader_AFR="${version}_AFR" | |
779 g1000_colheader_AMR="${version}_AMR" | |
780 g1000_colheader_ASN="${version}_ASN" | |
781 g1000_colheader_EUR="${version}_EUR" | |
5
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
782 g1000_colheader_EAS="${version}_EAS" |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
783 g1000_colheader_SAS="${version}_SAS" |
0 | 784 g1000_colheader_CEU="${version}_CEU" |
785 g1000_colheader_YRI="${version}_YRI" | |
786 g1000_colheader_JPTCHB="${version}_JPTCHB" | |
787 | |
788 doALL="N" | |
789 doAMR="N" | |
790 doAFR="N" | |
791 doASN="N" | |
5
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
792 doEAS="N" |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
793 doSAS="N" |
0 | 794 doEUR="N" |
795 doCEU="N" | |
796 doYRI="N" | |
797 doJPTCHB="N" | |
798 | |
799 | |
800 if [ $version == "1000g2012apr" ] | |
801 then | |
802 fileID="2012_04" | |
803 doALL="Y" | |
804 if [ $buildver == "hg19" ] | |
805 then | |
806 doAMR="Y" | |
807 doAFR="Y" | |
808 doASN="Y" | |
809 doEUR="Y" | |
5
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
810 fi |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
811 elif [ $version == "1000g2014oct" ] |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
812 then |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
813 fileID="2014_10" |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
814 doALL="Y" |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
815 doAMR="Y" |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
816 doAFR="Y" |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
817 doEUR="Y" |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
818 doEAS="Y" |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
819 if [ $buildver == "hg19" ] |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
820 then |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
821 doSAS="Y" |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
822 fi |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
823 |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
824 elif [[ $version == "1000g2015aug" && $buildver == "hg19" ]] |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
825 then |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
826 fileID="2015_08" |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
827 doALL="Y" |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
828 doAMR="Y" |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
829 doAFR="Y" |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
830 doEUR="Y" |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
831 doEAS="Y" |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
832 doSAS="Y" |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
833 |
0 | 834 elif [[ $version == "1000g2012feb" && $buildver == "hg19" ]] |
835 then | |
836 fileID="2012_02" | |
837 doALL="Y" | |
838 elif [[ $version == "1000g2010nov" && $buildver == "hg19" ]] | |
839 then | |
840 fileID="2010_11" | |
841 doALL="Y" | |
842 elif [[ $version == "1000g2010jul" && $buildver == "hg18" ]] | |
843 then | |
844 fileID="2010_07" | |
845 doALL="N" | |
846 doCEU="Y" | |
847 doYRI="Y" | |
848 doJPTCHB="Y" | |
849 else | |
850 echo "unrecognized 1000g version, skipping" | |
851 fi | |
852 | |
853 #ALL | |
854 if [ $doALL == "Y" ] | |
855 then | |
856 echo -e "\n1000Genomes ALL" | |
857 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype "${version}_all" annovarinput $humandb 2>&1 | |
858 | |
859 annovarout=annovarinput.${buildver}_ALL.sites.${fileID}_dropped | |
860 sed -i '1i\db\t'$g1000_colheader_ALL'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout | |
861 joinresults originalfile $annovarout 3 4 5 6 7 B.$g1000_colheader_ALL | |
862 fi | |
863 | |
864 # AFR | |
865 if [ $doAFR == "Y" ] | |
866 then | |
867 echo -e "\n1000Genomes AFR" | |
868 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype "${version}_afr" annovarinput $humandb 2>&1 | |
869 | |
870 annovarout=annovarinput.${buildver}_AFR.sites.${fileID}_dropped | |
871 sed -i '1i\db\t'$g1000_colheader_AFR'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout | |
872 joinresults originalfile $annovarout 3 4 5 6 7 B.$g1000_colheader_AFR | |
873 fi | |
874 | |
875 | |
876 # AMR | |
877 if [ $doAMR == "Y" ] | |
878 then | |
879 echo -e "\n1000Genomes AMR" | |
880 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype "${version}_amr" annovarinput $humandb 2>&1 | |
881 | |
882 annovarout=annovarinput.${buildver}_AMR.sites.${fileID}_dropped | |
883 sed -i '1i\db\t'$g1000_colheader_AMR'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout | |
884 joinresults originalfile $annovarout 3 4 5 6 7 B.$g1000_colheader_AMR | |
885 fi | |
886 | |
887 # ASN | |
888 if [ $doASN == "Y" ] | |
889 then | |
890 echo -e "\n1000Genomes ASN" | |
891 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype "${version}_asn" annovarinput $humandb 2>&1 | |
892 | |
893 annovarout=annovarinput.${buildver}_ASN.sites.${fileID}_dropped | |
894 sed -i '1i\db\t'$g1000_colheader_ASN'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout | |
895 joinresults originalfile $annovarout 3 4 5 6 7 B.$g1000_colheader_ASN | |
896 fi | |
5
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
897 |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
898 # EAS |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
899 if [ $doEAS == "Y" ] |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
900 then |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
901 echo -e "\n1000Genomes EAS" |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
902 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype "${version}_eas" annovarinput $humandb 2>&1 |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
903 |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
904 annovarout=annovarinput.${buildver}_EAS.sites.${fileID}_dropped |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
905 sed -i '1i\db\t'$g1000_colheader_EAS'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
906 joinresults originalfile $annovarout 3 4 5 6 7 B.$g1000_colheader_EAS |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
907 fi |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
908 |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
909 # SAS |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
910 if [ $doSAS == "Y" ] |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
911 then |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
912 echo -e "\n1000Genomes SAS" |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
913 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype "${version}_sas" annovarinput $humandb 2>&1 |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
914 |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
915 annovarout=annovarinput.${buildver}_SAS.sites.${fileID}_dropped |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
916 sed -i '1i\db\t'$g1000_colheader_SAS'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
917 joinresults originalfile $annovarout 3 4 5 6 7 B.$g1000_colheader_SAS |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
918 fi |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
919 |
0 | 920 # EUR |
921 if [ $doEUR == "Y" ] | |
922 then | |
923 echo -e "\n1000Genomes EUR" | |
924 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype "${version}_eur" annovarinput $humandb 2>&1 | |
925 | |
926 annovarout=annovarinput.${buildver}_EUR.sites.${fileID}_dropped | |
927 sed -i '1i\db\t'$g1000_colheader_EUR'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout | |
928 joinresults originalfile $annovarout 3 4 5 6 7 B.$g1000_colheader_EUR | |
929 fi | |
930 | |
931 # CEU | |
932 if [ $doCEU == "Y" ] | |
933 then | |
934 echo -e "\n1000Genomes CEU" | |
935 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype "${version}_ceu" annovarinput $humandb 2>&1 | |
936 | |
937 annovarout=annovarinput.${buildver}_CEU.sites.${fileID}_dropped | |
938 sed -i '1i\db\t'$g1000_colheader_CEU'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout | |
939 joinresults originalfile $annovarout 3 4 5 6 7 B.$g1000_colheader_CEU | |
940 fi | |
941 | |
942 # YRI | |
943 if [ $doYRI == "Y" ] | |
944 then | |
945 echo -e "\n1000Genomes YRI" | |
946 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype "${version}_yri" annovarinput $humandb 2>&1 | |
947 | |
948 annovarout=annovarinput.${buildver}_YRI.sites.${fileID}_dropped | |
949 sed -i '1i\db\t'$g1000_colheader_YRI'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout | |
950 joinresults originalfile $annovarout 3 4 5 6 7 B.$g1000_colheader_YRI | |
951 | |
952 | |
953 fi | |
954 | |
955 #JPTCHB | |
956 if [ $doJPTCHB == "Y" ] | |
957 then | |
958 echo -e "\n1000Genomes JPTCHB" | |
959 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype "${version}_jptchb" annovarinput $humandb 2>&1 | |
960 | |
961 annovarout=annovarinput.${buildver}_JPTCHB.sites.${fileID}_dropped | |
962 sed -i '1i\db\t'$g1000_colheader_JPTCHB'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout | |
963 joinresults originalfile $annovarout 3 4 5 6 7 B.$g1000_colheader_JPTCHB | |
964 fi | |
965 | |
966 done | |
967 fi | |
968 | |
969 | |
2
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
970 |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
971 |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
972 #### IMPACT SCORE ANNOTATIONS |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
973 |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
974 |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
975 if [ $ljb2_sift == "Y" ] |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
976 then |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
977 echo -e "\nLJB2 SIFT Annotation" |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
978 $scriptsdir/annotate_variation.pl --filter --buildver $buildver $otherinfo -dbtype ljb2_sift annovarinput $humandb 2>&1 |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
979 |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
980 annovarout=annovarinput.${buildver}_ljb2_sift_dropped |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
981 sed -i '1i\db\tLJB2_SIFT\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
982 joinresults originalfile $annovarout 3 4 5 6 7 B.LJB2_SIFT |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
983 fi |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
984 |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
985 if [ $ljb2_pp2hdiv == "Y" ] |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
986 then |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
987 echo -e "\nLJB2 pp2hdiv Annotation" |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
988 $scriptsdir/annotate_variation.pl --filter --buildver $buildver $otherinfo -dbtype ljb2_pp2hdiv annovarinput $humandb 2>&1 |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
989 |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
990 annovarout=annovarinput.${buildver}_ljb2_pp2hdiv_dropped |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
991 sed -i '1i\db\tLJB2_PolyPhen2_HDIV\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
992 joinresults originalfile $annovarout 3 4 5 6 7 B.LJB2_PolyPhen2_HDIV |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
993 fi |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
994 |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
995 if [ $ljb2_pp2hvar == "Y" ] |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
996 then |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
997 echo -e "\nLJB2 pp2hvar Annotation" |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
998 $scriptsdir/annotate_variation.pl --filter --buildver $buildver $otherinfo -dbtype ljb2_pp2hvar annovarinput $humandb 2>&1 |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
999 |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1000 annovarout=annovarinput.${buildver}_ljb2_pp2hvar_dropped |
5
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1001 |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1002 head $annovarout |
2
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1003 sed -i '1i\db\tLJB2_PolyPhen2_HVAR\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1004 joinresults originalfile $annovarout 3 4 5 6 7 B.LJB2_PolyPhen2_HVAR |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1005 fi |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1006 |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1007 if [ $ljb2_lrt == "Y" ] |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1008 then |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1009 echo -e "\nLJB2 LRT Annotation" |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1010 $scriptsdir/annotate_variation.pl --filter --buildver $buildver $otherinfo -dbtype ljb2_lrt annovarinput $humandb 2>&1 |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1011 |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1012 annovarout=annovarinput.${buildver}_ljb2_lrt_dropped |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1013 sed -i '1i\db\tLJB2_LRT\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1014 joinresults originalfile $annovarout 3 4 5 6 7 B.LJB2_LRT |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1015 fi |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1016 |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1017 if [ $ljb2_mt == "Y" ] |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1018 then |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1019 echo -e "\nLJB2 mutationtaster Annotation" |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1020 $scriptsdir/annotate_variation.pl --filter --buildver $buildver $otherinfo -dbtype ljb2_mt annovarinput $humandb 2>&1 |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1021 |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1022 annovarout=annovarinput.${buildver}_ljb2_mt_dropped |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1023 sed -i '1i\db\tLJB2_MutationTaster\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1024 joinresults originalfile $annovarout 3 4 5 6 7 B.LJB2_MutationTaster |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1025 fi |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1026 |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1027 if [ $ljb2_ma == "Y" ] |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1028 then |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1029 echo -e "\nLJB2 mutationassessor Annotation" |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1030 $scriptsdir/annotate_variation.pl --filter --buildver $buildver $otherinfo -dbtype ljb2_ma annovarinput $humandb 2>&1 |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1031 |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1032 annovarout=annovarinput.${buildver}_ljb2_ma_dropped |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1033 sed -i '1i\db\tLJB2_MutationAssessor\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1034 joinresults originalfile $annovarout 3 4 5 6 7 B.LJB2_MutationAssessor |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1035 fi |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1036 |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1037 if [ $ljb2_fathmm == "Y" ] |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1038 then |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1039 echo -e "\nLJB2 FATHMM Annotation" |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1040 $scriptsdir/annotate_variation.pl --filter --buildver $buildver $otherinfo -dbtype ljb2_fathmm annovarinput $humandb 2>&1 |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1041 |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1042 annovarout=annovarinput.${buildver}_ljb2_fathmm_dropped |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1043 sed -i '1i\db\tLJB2_FATHMM\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1044 joinresults originalfile $annovarout 3 4 5 6 7 B.LJB2_FATHMM |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1045 fi |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1046 |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1047 if [ $ljb2_gerp == "Y" ] |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1048 then |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1049 echo -e "\nLJB2 GERP++ Annotation" |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1050 $scriptsdir/annotate_variation.pl --filter --buildver $buildver $otherinfo -dbtype ljb2_gerp++ annovarinput $humandb 2>&1 |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1051 |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1052 annovarout=annovarinput.${buildver}_ljb2_gerp++_dropped |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1053 sed -i '1i\db\tLJB2_GERP++\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1054 joinresults originalfile $annovarout 3 4 5 6 7 B.LJB2_GERP++ |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1055 fi |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1056 |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1057 if [ $ljb2_phylop == "Y" ] |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1058 then |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1059 echo -e "\nLJB2 PhyloP Annotation" |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1060 $scriptsdir/annotate_variation.pl --filter --buildver $buildver $otherinfo -dbtype ljb2_phylop annovarinput $humandb 2>&1 |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1061 |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1062 annovarout=annovarinput.${buildver}_ljb2_phylop_dropped |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1063 sed -i '1i\db\tLJB2_PhyloP\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1064 joinresults originalfile $annovarout 3 4 5 6 7 B.LJB2_PhyloP |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1065 fi |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1066 |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1067 if [ $ljb2_siphy == "Y" ] |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1068 then |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1069 echo -e "\nLJB2 SiPhy Annotation" |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1070 $scriptsdir/annotate_variation.pl --filter --buildver $buildver $otherinfo -dbtype ljb2_siphy annovarinput $humandb 2>&1 |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1071 |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1072 annovarout=annovarinput.${buildver}_ljb2_siphy_dropped |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1073 sed -i '1i\db\tLJB2_SiPhy\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1074 joinresults originalfile $annovarout 3 4 5 6 7 B.LJB2_SiPhy |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1075 fi |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1076 |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1077 |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1078 |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1079 ### OLD IMPACT SCORE ANNOTATIONS |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1080 |
0 | 1081 # SIFT |
1082 if [ $avsift == "Y" ] | |
1083 then | |
1084 echo -e "\nSIFT Annotation" | |
1085 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype avsift annovarinput $humandb 2>&1 | |
1086 | |
1087 annovarout=annovarinput.${buildver}_avsift_dropped | |
1088 sed -i '1i\db\tAVSIFT\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout | |
1089 joinresults originalfile $annovarout 3 4 5 6 7 B.AVSIFT | |
1090 fi | |
1091 | |
1092 #ljb refers to Liu, Jian, Boerwinkle paper in Human Mutation with pubmed ID 21520341. Cite this paper if you use the scores | |
1093 # SIFT2 | |
1094 if [ $ljbsift == "Y" ] | |
1095 then | |
2
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1096 echo -e "\nLJB SIFT Annotation" |
0 | 1097 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype ljb_sift annovarinput $humandb 2>&1 |
1098 | |
1099 annovarout=annovarinput.${buildver}_ljb_sift_dropped | |
1100 sed -i '1i\db\tLJB_SIFT\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout | |
1101 joinresults originalfile $annovarout 3 4 5 6 7 B.LJB_SIFT | |
1102 fi | |
1103 | |
1104 | |
1105 # PolyPhen2 | |
1106 if [ $polyphen2 == "Y" ] | |
1107 then | |
1108 echo -e "\nPolyPhen Annotation" | |
1109 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype ljb_pp2 annovarinput $humandb 2>&1 | |
1110 | |
1111 annovarout=annovarinput.${buildver}_ljb_pp2_dropped | |
1112 sed -i '1i\db\tPolyPhen2\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout | |
1113 joinresults originalfile $annovarout 3 4 5 6 7 B.PolyPhen2 | |
1114 fi | |
1115 | |
1116 | |
1117 # MutationTaster | |
1118 if [ $mutationtaster == "Y" ] | |
1119 then | |
1120 echo -e "\nMutationTaster Annotation" | |
1121 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype ljb_mt annovarinput $humandb 2>&1 | |
1122 | |
1123 annovarout=annovarinput.${buildver}_ljb_mt_dropped | |
1124 sed -i '1i\db\tMutationTaster\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout | |
1125 joinresults originalfile $annovarout 3 4 5 6 7 B.MutationTaster | |
1126 fi | |
1127 | |
1128 | |
1129 # LRT | |
1130 if [ $lrt == "Y" ] | |
1131 then | |
1132 echo -e "\nLRT Annotation" | |
1133 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype ljb_lrt annovarinput $humandb 2>&1 | |
1134 | |
1135 annovarout=annovarinput.${buildver}_ljb_lrt_dropped | |
1136 sed -i '1i\db\tLikelihoodRatioTestScore\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout | |
1137 joinresults originalfile $annovarout 3 4 5 6 7 B.LikelihoodRatioTestScore | |
1138 fi | |
1139 | |
1140 # PhyloP | |
1141 if [ $phylop == "Y" ] | |
1142 then | |
1143 echo -e "\nPhyloP Annotation" | |
1144 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype ljb_phylop annovarinput $humandb 2>&1 | |
1145 | |
1146 annovarout=annovarinput.${buildver}_ljb_phylop_dropped | |
1147 sed -i '1i\db\tPhyloP\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout | |
1148 joinresults originalfile $annovarout 3 4 5 6 7 B.PhyloP | |
1149 fi | |
1150 | |
1151 | |
1152 ### ESP Exome Variant Server | |
1153 if [ $esp != "None" ] | |
1154 then | |
1155 echo -e "\nESP Annotation" | |
1156 for version in $espstr | |
1157 do | |
1158 echo "version: $version" | |
1159 # 6500si ALL | |
1160 if [ $version == "esp6500si_all" ] | |
1161 then | |
1162 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype esp6500si_all annovarinput $humandb 2>&1 | |
1163 | |
1164 annovarout=annovarinput.${buildver}_esp6500si_all_dropped | |
1165 sed -i '1i\db\t'$esp6500si_colheader_ALL'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout | |
1166 joinresults originalfile $annovarout 3 4 5 6 7 B.$esp6500si_colheader_ALL | |
1167 fi | |
1168 | |
1169 | |
1170 # 6500si European American | |
1171 if [ $version == "esp6500si_ea" ] | |
1172 then | |
1173 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype esp6500si_ea annovarinput $humandb 2>&1 | |
1174 | |
1175 annovarout=annovarinput.${buildver}_esp6500si_ea_dropped | |
1176 sed -i '1i\db\t'$esp6500si_colheader_EA'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'" ' $annovarout | |
1177 joinresults originalfile $annovarout 3 4 5 6 7 B.$esp6500si_colheader_EA | |
1178 fi | |
1179 | |
1180 # 6500si African Americans | |
1181 if [ $version == "esp6500si_aa" ] | |
1182 then | |
1183 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype esp6500si_aa annovarinput $humandb 2>&1 | |
1184 | |
1185 annovarout=annovarinput.${buildver}_esp6500si_aa_dropped | |
1186 sed -i '1i\db\t'$esp6500si_colheader_AA'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'" ' $annovarout | |
1187 joinresults originalfile $annovarout 3 4 5 6 7 B.$esp6500si_colheader_AA | |
1188 fi | |
1189 | |
1190 | |
1191 # 6500 ALL | |
1192 if [ $version == "esp6500_all" ] | |
1193 then | |
1194 ls | |
1195 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype esp6500_all annovarinput $humandb 2>&1 | |
1196 | |
1197 annovarout=annovarinput.${buildver}_esp6500_all_dropped | |
1198 sed -i '1i\db\t'$esp6500_colheader_ALL'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'" ' $annovarout | |
1199 joinresults originalfile $annovarout 3 4 5 6 7 B.$esp6500_colheader_ALL | |
1200 fi | |
1201 | |
1202 | |
1203 # 6500 European American | |
1204 if [ $version == "esp6500_ea" ] | |
1205 then | |
1206 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype esp6500_ea annovarinput $humandb 2>&1 | |
1207 annovarout=annovarinput.${buildver}_esp6500_ea_dropped | |
1208 sed -i '1i\db\t'$esp6500_colheader_EA'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout | |
1209 joinresults originalfile $annovarout 3 4 5 6 7 B.$esp6500_colheader_EA | |
1210 fi | |
1211 | |
1212 # 6500 African Americans | |
1213 if [ $version == "esp6500_aa" ] | |
1214 then | |
1215 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype esp6500_aa annovarinput $humandb 2>&1 | |
1216 | |
1217 annovarout=annovarinput.${buildver}_esp6500_aa_dropped | |
1218 sed -i '1i\db\t'$esp6500_colheader_AA'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout | |
1219 joinresults originalfile $annovarout 3 4 5 6 7 B.$esp6500_colheader_AA | |
1220 fi | |
1221 | |
1222 | |
1223 # 5400 ALL | |
1224 if [ $version == "esp5400_all" ] | |
1225 then | |
1226 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype esp5400_all annovarinput $humandb 2>&1 | |
1227 | |
1228 annovarout=annovarinput.${buildver}_esp5400_all_dropped | |
1229 sed -i '1i\db\t'$esp5400_colheader_ALL'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout | |
1230 joinresults originalfile $annovarout 3 4 5 6 7 B.$esp5400_colheader_ALL | |
1231 fi | |
1232 | |
1233 | |
1234 # 5400 European American | |
1235 if [ $version == "esp5400_ea" ] | |
1236 then | |
1237 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype esp5400_ea annovarinput $humandb 2>&1 | |
1238 | |
1239 annovarout=annovarinput.${buildver}_esp5400_ea_dropped | |
1240 sed -i '1i\db\t'$esp5400_colheader_EA'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout | |
1241 joinresults originalfile $annovarout 3 4 5 6 7 B.$esp5400_colheader_EA | |
1242 fi | |
1243 | |
1244 # 5400 African Americans | |
1245 if [ $version == "esp5400_aa" ] | |
1246 then | |
1247 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype esp5400_aa annovarinput $humandb 2>&1 | |
1248 | |
1249 annovarout=annovarinput.${buildver}_esp5400_aa_dropped | |
1250 sed -i '1i\db\t'$esp5400_colheader_AA'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout | |
1251 joinresults originalfile $annovarout 3 4 5 6 7 B.$esp5400_colheader_AA | |
1252 fi | |
1253 | |
1254 done | |
1255 fi | |
1256 | |
5
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1257 |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1258 #ExAC-03 database |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1259 if [ $exac03 == "Y" ] |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1260 then |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1261 echo -e "\nExAC03 Annotation" |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1262 $scriptsdir/annotate_variation.pl --filter -otherinfo --buildver $buildver --otherinfo -dbtype exac03 annovarinput $humandb 2>&1 |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1263 |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1264 #annovarout=annovarinput.${buildver}_exac03_dropped |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1265 |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1266 # split allelefrequency column into several columns, one per population |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1267 awk 'BEGIN{FS="\t" |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1268 OFS="\t" |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1269 }{ |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1270 gsub(",","\t",$2) |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1271 print $0 |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1272 }END{}' annovarinput.${buildver}_exac03_dropped > $annovarout |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1273 |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1274 sed -i '1i\db\tExAC_Freq\tExAC_AFR\tExAC_AMR\tExAC_EAS\tExAC_FIN\tExAC_NFE\tExAC_OTH\tExAC_SAS\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1275 joinresults originalfile $annovarout 10 11 12 13 14 B.ExAC_Freq,B.ExAC_AFR,B.ExAC_AMR,B.ExAC_EAS,B.ExAC_FIN,B.ExAC_NFE,B.ExAC_OTH,B.ExAC_SAS |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1276 fi |
0 | 1277 |
5
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1278 #GoNL database |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1279 if [ $gonl == "Y" ] |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1280 then |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1281 |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1282 if [ $buildver == "hg19" ] |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1283 then |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1284 echo -e "\nGoNL Annotation" |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1285 $scriptsdir/annotate_variation.pl --filter --buildver $buildver --otherinfo -dbtype generic -genericdbfile ${buildver}_gonl.txt annovarinput $humandb 2>&1 |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1286 |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1287 ls |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1288 annovarout=annovarinput.${buildver}_generic_dropped |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1289 |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1290 head $annovarout |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1291 |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1292 sed -i '1i\db\tGoNL\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1293 joinresults originalfile $annovarout 3 4 5 6 7 B.GoNL |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1294 |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1295 fi |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1296 |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1297 fi |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1298 |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1299 #SPIDEX database |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1300 if [ $spidex == "Y" ] |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1301 then |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1302 |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1303 if [ $buildver == "hg19" ] |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1304 then |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1305 echo -e "\nSPIDEX Annotation" |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1306 $scriptsdir/annotate_variation.pl --filter --buildver $buildver --otherinfo -dbtype spidex annovarinput $humandb 2>&1 |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1307 |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1308 # split allelefrequency column into several columns, one per population |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1309 awk 'BEGIN{FS="\t" |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1310 OFS="\t" |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1311 }{ |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1312 gsub(",","\t",$2) |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1313 print $0 |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1314 }END{}' annovarinput.${buildver}_spidex_dropped > $annovarout |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1315 |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1316 #annovarout=annovarinput.${buildver}_spidex_dropped |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1317 #head $annovarout |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1318 |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1319 sed -i '1i\db\tSPIDEX_dpsi_max_tissue\tSPIDEX_dpsi_zscore\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1320 joinresults originalfile $annovarout 4 5 6 7 8 B.SPIDEX_dpsi_max_tissue,B.SPIDEX_dpsi_zscore |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1321 |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1322 fi |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1323 |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1324 fi |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1325 |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1326 |
0 | 1327 #GERP++ |
1328 if [ $gerp == "Y" ] | |
1329 then | |
1330 echo -e "\nGERP++ Annotation" | |
1331 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype gerp++gt2 annovarinput $humandb 2>&1 | |
1332 | |
1333 annovarout="annovarinput.${buildver}_gerp++gt2_dropped" | |
1334 sed -i '1i\db\tGERP++\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout | |
1335 joinresults originalfile $annovarout 3 4 5 6 7 B.GERP++ | |
1336 fi | |
1337 | |
1338 | |
1339 #COSMIC | |
1340 if [[ $cosmic61 == "Y" && $buildver == "hg19" ]] | |
1341 then | |
1342 echo -e "\nCOSMIC61 Annotation" | |
1343 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype cosmic61 annovarinput $humandb 2>&1 | |
1344 | |
1345 annovarout="annovarinput.${buildver}_cosmic61_dropped" | |
1346 sed -i '1i\db\tCOSMIC61\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout | |
1347 joinresults originalfile $annovarout 3 4 5 6 7 B.COSMIC61 | |
1348 | |
1349 fi | |
1350 | |
1351 if [[ $cosmic63 == "Y" && $buildver == "hg19" ]] | |
1352 then | |
1353 echo -e "\nCOSMIC63 Annotation" | |
1354 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype cosmic63 annovarinput $humandb 2>&1 | |
1355 | |
1356 annovarout="annovarinput.${buildver}_cosmic63_dropped" | |
1357 sed -i '1i\db\tCOSMIC63\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout | |
1358 joinresults originalfile $annovarout 3 4 5 6 7 B.COSMIC63 | |
1359 | |
1360 fi | |
1361 | |
1362 if [[ $cosmic64 == "Y" && $buildver == "hg19" ]] | |
1363 then | |
1364 echo -e "\nCOSMIC64 Annotation" | |
1365 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype cosmic64 annovarinput $humandb 2>&1 | |
1366 | |
1367 annovarout="annovarinput.${buildver}_cosmic64_dropped" | |
1368 sed -i '1i\db\tCOSMIC64\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout | |
1369 joinresults originalfile $annovarout 3 4 5 6 7 B.COSMIC64 | |
1370 | |
1371 fi | |
1372 | |
1373 if [[ $cosmic65 == "Y" && $buildver == "hg19" ]] | |
1374 then | |
1375 echo -e "\nCOSMIC65 Annotation" | |
1376 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype cosmic65 annovarinput $humandb 2>&1 | |
1377 | |
1378 annovarout="annovarinput.${buildver}_cosmic65_dropped" | |
1379 sed -i '1i\db\tCOSMIC65\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout | |
1380 joinresults originalfile $annovarout 3 4 5 6 7 B.COSMIC65 | |
1381 | |
1382 fi | |
1383 | |
2
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1384 if [[ $cosmic67 == "Y" && $buildver == "hg19" ]] |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1385 then |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1386 echo -e "\nCOSMIC67 Annotation" |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1387 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype cosmic67 annovarinput $humandb 2>&1 |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1388 |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1389 annovarout="annovarinput.${buildver}_cosmic67_dropped" |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1390 sed -i '1i\db\tCOSMIC67\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1391 joinresults originalfile $annovarout 3 4 5 6 7 B.COSMIC67 |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1392 |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1393 fi |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1394 |
3 | 1395 if [[ $cosmic68 == "Y" && $buildver == "hg19" ]] |
1396 then | |
1397 echo -e "\nCOSMIC68 Annotation" | |
1398 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype cosmic68 annovarinput $humandb 2>&1 | |
1399 | |
1400 annovarout="annovarinput.${buildver}_cosmic68_dropped" | |
1401 sed -i '1i\db\tCOSMIC68\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout | |
1402 joinresults originalfile $annovarout 3 4 5 6 7 B.COSMIC68 | |
1403 | |
1404 fi | |
1405 | |
5
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1406 if [[ $cosmic70 == "Y" && $buildver == "hg19" ]] |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1407 then |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1408 echo -e "\nCOSMIC70 Annotation" |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1409 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype cosmic70 annovarinput $humandb 2>&1 |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1410 |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1411 annovarout="annovarinput.${buildver}_cosmic70_dropped" |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1412 sed -i '1i\db\tCOSMIC70\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1413 joinresults originalfile $annovarout 3 4 5 6 7 B.COSMIC70 |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1414 |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1415 fi |
3 | 1416 |
2
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1417 if [[ $clinvar == "Y" && $buildver == "hg19" ]] |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1418 then |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1419 echo -e "\nCLINVAR Annotation" |
3 | 1420 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype clinvar_20140211 annovarinput $humandb 2>&1 |
2
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1421 |
3 | 1422 annovarout="annovarinput.${buildver}_clinvar_20140211_dropped" |
2
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1423 sed -i '1i\db\tCLINVAR\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1424 joinresults originalfile $annovarout 3 4 5 6 7 B.CLINVAR |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1425 |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1426 fi |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1427 |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1428 if [[ $nci60 == "Y" && $buildver == "hg19" ]] |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1429 then |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1430 echo -e "\nNCI60 Annotation" |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1431 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype nci60 annovarinput $humandb 2>&1 |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1432 |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1433 annovarout="annovarinput.${buildver}_nci60_dropped" |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1434 sed -i '1i\db\tNCI60\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1435 joinresults originalfile $annovarout 3 4 5 6 7 B.NCI60 |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1436 |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1437 fi |
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1438 |
0 | 1439 #cg46 |
1440 if [[ $cg46 == "Y" ]] | |
1441 then | |
1442 echo -e "\nCG 46 genomes Annotation" | |
1443 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype cg46 annovarinput $humandb 2>&1 | |
1444 | |
1445 annovarout="annovarinput.${buildver}_cg46_dropped" | |
1446 sed -i '1i\db\t'${cg46_colheader}'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout | |
1447 joinresults originalfile $annovarout 3 4 5 6 7 B.${cg46_colheader} | |
1448 | |
1449 fi | |
1450 | |
1451 | |
1452 #cg69 | |
1453 if [[ $cg69 == "Y" ]] | |
1454 then | |
1455 echo -e "\nCG 69 genomes Annotation" | |
1456 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype cg69 annovarinput $humandb 2>&1 | |
1457 | |
1458 annovarout="annovarinput.${buildver}_cg69_dropped" | |
1459 sed -i '1i\db\t'${cg69_colheader}'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout | |
1460 joinresults originalfile $annovarout 3 4 5 6 7 B.${cg69_colheader} | |
1461 | |
1462 fi | |
1463 | |
1464 | |
1465 | |
1466 if [ $convertcoords == "Y" ] | |
1467 then | |
1468 echo "converting back coordinates" | |
1469 awk 'BEGIN{ | |
1470 FS="\t"; | |
1471 OFS="\t"; | |
1472 }{ | |
1473 if (FNR==1) | |
1474 print $0 | |
1475 if(FNR>1) { | |
1476 $"'"${chrcol}"'" = "chr"$"'"${chrcol}"'" | |
1477 if( $"'"${vartypecol}"'" == "snp" ){ $"'"${startcol}"'" -= 1 }; | |
1478 if( $"'"${vartypecol}"'" == "ins" ){ $"'"${refcol}"'" = "" }; | |
1479 if( $"'"${vartypecol}"'" == "del" ){ $"'"${startcol}"'" -=1; $"'"${obscol}"'" = "" }; | |
1480 if( $"'"${vartypecol}"'" == "sub" ){ $"'"${startcol}"'" -= 1 }; | |
1481 print $0 | |
1482 | |
1483 } | |
1484 } | |
1485 END{ | |
1486 }' originalfile > originalfile_coords | |
1487 else | |
1488 mv originalfile originalfile_coords | |
1489 fi | |
1490 | |
1491 #restore "chr" prefix? | |
1492 | |
1493 #move to outputfile | |
1494 if [ ! -s annovarinput.invalid_input ] | |
1495 then | |
1496 echo "Congrats, your input file contained no invalid lines!" > annovarinput.invalid_input | |
1497 fi | |
1498 | |
1499 cp originalfile_coords $outfile_all | |
1500 cp annovarinput.invalid_input $outfile_invalid 2>&1 | |
5
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1501 |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1502 sed -i 's/chrchr/chr/g' $outfile_all |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1503 sed -i 's/chrchr/chr/g' $outfile_invalid |
4600be69b96f
Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
3
diff
changeset
|
1504 |
0 | 1505 fi #if $dorunannovar |
1506 | |
1507 | |
1508 | |
1509 | |
1510 | |
1511 | |
1512 | |
1513 | |
1514 | |
1515 | |
1516 | |
1517 | |
1518 | |
1519 | |
1520 | |
1521 | |
1522 | |
1523 | |
1524 | |
1525 | |
1526 | |
1527 | |
2
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
1528 |