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comparison gfapts/gfap_r1.0_known_var_finder.xml @ 0:f753b30013e6 draft

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author rdaveau
date Fri, 29 Jun 2012 10:20:55 -0400
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1 <tool id="gfap_r1.0_known_var_finder" name="Known variants finder">
2 <description>Search the GFAP database for known variants</description>
3 <command interpreter="perl">gfap_r1.0_known_var_finder.pl -varfile=$varfile -buildver=$buildver -outdir=$__new_file_path__/gfap -dir_1000g=db/1000g -dir_dbsnp=db/dbsnp -dir_cosmic=db/cosmic -release_1000g=$release_1000g -release_dbsnp=$release_dbsnp -release_cosmic=$release_cosmic -outfile=$outfile</command>
4 <inputs>
5 <param name="varfile" format="txt" type="data" label="Input VAR file" />
6 <param name="buildver" type="select" label="Human reference genome assembly">
7 <option value="hg19">GRCh37 ie. hg19</option>
8 </param>
9 <param name="release_1000g" type="select" label="1000 Genomes data release">
10 <option value="phase1_20101123">phase 1 r20101123 </option>
11 </param>
12 <param name="release_dbsnp" type="select" label="dbSNP data release">
13 <option value="v135">v135</option>
14 </param>
15 <param name="release_cosmic" type="select" label="COSMIC data release">
16 <option value="v56">v56</option>
17 </param>
18 </inputs>
19 <outputs>
20 <data format="txt" name="outfile" label="${varfile.name}.dbi" />
21 </outputs>
22 <help>
23 .. class:: infomark
24
25 **What it does**
26
27 Annotate a VAR-file with **1000G**, **dbSNP** and **COSMIC** data.
28
29 - This VAR-file has to be generated by the **SAMVCF_data_parser** gfap utility.
30 - Included in the gfap archive, variant databases mentioned ahead consist in **built-in pre-processed flat files**.
31
32 .. class:: infomark
33
34 **Third-party resources**
35
36 - 1000G: http://www.1000genomes.org
37 - dbSNP: http://www.ncbi.nlm.nih.gov/projects/SNP
38 - COSMIC: http://www.sanger.ac.uk/genetics/CGP/cosmic
39
40 ----
41
42 **Input .var file**::
43
44 #chr start end ref alt ann QC NRF NRR NAF NAR VCF.FILTER P.str P.ref P.alt DP AD AF VAR.FILTER
45 chr1 14907 14907 A G het 9 4 0 0 3 NONE 3.33e-01 4.17e-02 8.33e-02 7 3 0.4290 SKIP
46 chr1 14930 14930 A G het 37 4 2 0 5 NONE 1.83e-01 2.29e-01 2.08e-02 11 5 0.4550 SKIP
47 chr1 68896 68896 G A hom 18 0 0 3 0 NONE 8.33e-02 3.33e-01 8.33e-02 3 3 1.0000 SKIP
48 chr1 69270 69270 A G hom 179 0 0 31 0 NONE 3.10e-10 3.33e-01 3.10e-10 31 31 1.0000 SKIP
49 chr1 69511 69511 A G hom 222 0 0 13 12 NONE 3.33e-01 3.33e-01 3.33e-01 25 25 1.0000 PASS
50 chr1 69897 69897 T C het 14 1 0 0 3 NONE 2.08e-01 3.33e-01 8.33e-02 4 3 0.7500 SKIP
51 chr1 129285 129285 G A het 56 0 4 0 4 NONE 2.60e-03 4.17e-02 4.17e-02 8 4 0.5000 SKIP
52 chr1 567697 567697 G A hom 30 0 0 0 2 NONE 1.67e-01 3.33e-01 1.67e-01 2 2 1.0000 SKIP
53 chr1 569803 569803 G A hom 50 0 0 4 0 NONE 4.17e-02 3.33e-01 4.17e-02 4 4 1.0000 SKIP
54 chr1 808631 808631 G A hom 142 0 0 7 1 NONE 2.34e-02 3.33e-01 2.34e-02 8 8 1.0000 SKIP
55 chr1 808922 808922 G A hom 222 0 0 15 26 NONE 3.91e-02 3.33e-01 3.91e-02 41 41 1.0000 PASS
56 chr1 808928 808928 C T hom 222 0 0 14 31 NONE 5.36e-03 3.33e-01 5.36e-03 45 45 1.0000 PASS
57 chr1 816725 816725 A G hom 22 0 0 2 0 NONE 1.67e-01 3.33e-01 1.67e-01 2 2 1.0000 SKIP
58 chr1 821030 821030 G T hom 36 0 0 2 0 NONE 1.67e-01 3.33e-01 1.67e-01 2 2 1.0000 SKIP
59 chr1 821143 821143 G T hom 8 0 0 0 2 NONE 1.67e-01 3.33e-01 1.67e-01 2 2 1.0000 SKIP
60
61 ----
62
63 **Output .dbi file**::
64
65 #From [chr] to [VAR.FILTER] = VAR file header; DPT.FILTER = check for heterogeneous depth in substituted blocks
66 #AF_ALL = global AF in phase1_20101123 1000g data
67 #AF_AFR = AF in AFR phase1_20101123 1000g data
68 #AF_AMR = AF in AMR phase1_20101123 1000g data
69 #AF_ASN = AF in ASN phase1_20101123 1000g data
70 #AF_EUR = AF in EUR phase1_20101123 1000g data
71 #AF_COS = AF in v56 cosmic data
72 #cid = cosmic mutation identifier from v56 release
73 #rs = dbsnp rs identifier(s) from v135 release
74 #dbsnp = dbsnp build version(s) from v135 release
75 #chr start end ref alt NRF NRR NAF NAR DP AD AF QC P.str P.ref P.alt VCF.FILTER DPT.FILTER VAR.FILTER AF_ALL AF_AFR AF_AMR AF_ASN AF_EUR AF_COS cid rs dbsnp
76 chr1 14907 14907 A G 4 0 0 3 7 3 0.4290 9 3.33e-01 4.17e-02 8.33e-02 NONE PASS SKIP 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 na na na
77 chr1 14930 14930 A G 4 2 0 5 11 5 0.4550 37 1.83e-01 2.29e-01 2.08e-02 NONE PASS SKIP 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 na na na
78 chr1 68896 68896 G A 0 0 3 0 3 3 1.0000 18 8.33e-02 3.33e-01 8.33e-02 NONE PASS SKIP 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 na na na
79 chr1 69270 69270 A G 0 0 31 0 31 31 1.0000 179 3.10e-10 3.33e-01 3.10e-10 NONE PASS SKIP 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 na na na
80 chr1 69511 69511 A G 0 0 13 12 25 25 1.0000 222 3.33e-01 3.33e-01 3.33e-01 NONE PASS PASS 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 na na na
81 chr1 69897 69897 T C 1 0 0 3 4 3 0.7500 14 2.08e-01 3.33e-01 8.33e-02 NONE PASS SKIP 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 na na na
82 chr1 129285 129285 G A 0 4 0 4 8 4 0.5000 56 2.60e-03 4.17e-02 4.17e-02 NONE PASS SKIP 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 na na na
83 chr1 567697 567697 G A 0 0 0 2 2 2 1.0000 30 1.67e-01 3.33e-01 1.67e-01 NONE PASS SKIP 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 na na na
84 chr1 569803 569803 G A 0 0 4 0 4 4 1.0000 50 4.17e-02 3.33e-01 4.17e-02 NONE PASS SKIP 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 na na na
85 chr1 808631 808631 G A 0 0 7 1 8 8 1.0000 142 2.34e-02 3.33e-01 2.34e-02 NONE PASS SKIP 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 na na na
86 chr1 808922 808922 G A 0 0 15 26 41 41 1.0000 222 3.91e-02 3.33e-01 3.91e-02 NONE PASS PASS 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 na na na
87 chr1 808928 808928 C T 0 0 14 31 45 45 1.0000 222 5.36e-03 3.33e-01 5.36e-03 NONE PASS PASS 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 na na na
88 chr1 816725 816725 A G 0 0 2 0 2 2 1.0000 22 1.67e-01 3.33e-01 1.67e-01 NONE PASS SKIP 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 na na na
89 chr1 821030 821030 G T 0 0 2 0 2 2 1.0000 36 1.67e-01 3.33e-01 1.67e-01 NONE PASS SKIP 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 na na na
90 chr1 821143 821143 G T 0 0 0 2 2 2 1.0000 8 1.67e-01 3.33e-01 1.67e-01 NONE PASS SKIP 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 na na na
91
92 ----
93
94 .. class:: infomark
95
96 **Feedback**: romain.daveau@curie.fr
97 </help>
98 </tool>