Mercurial > repos > rdaveau > gfap
comparison gfapts/gfap_r1.0_allvar_genomic_annotater.xml @ 0:f753b30013e6 draft
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author | rdaveau |
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date | Fri, 29 Jun 2012 10:20:55 -0400 |
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1 <tool id="gfap_r1.0_allvar_genomic_annotater" name="Map to genomic features"> | |
2 <description>Annotate variants with ANNOVAR</description> | |
3 <command interpreter="perl">gfap_r1.0_allvar_genomic_annotater.pl -varfile=$varfile -buildver=$buildver -refseq_dir=db/refseq -refseq_release=$refseq_release -cosmic_dir=db/cosmic -cosmic_release=$cosmic_release -annovar_release=$annovar_release -outdir=$__new_file_path__/gfap -noncoding=$noncoding -coding=$coding</command> | |
4 <inputs> | |
5 <param name="varfile" format="txt" type="data" label="Input VAR or DBI 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="refseq_release" type="select" label="human.protein.gpff release"> | |
10 <option value="r16012012">Jan 16, 2012</option> | |
11 </param> | |
12 <param name="cosmic_release" type="select" label="COSMIC db release"> | |
13 <option value="v56">v56</option> | |
14 </param> | |
15 <param name="annovar_release" type="select" label="ANNOVAR db release"> | |
16 <option value="jan2012">Jan 2012</option> | |
17 </param> | |
18 </inputs> | |
19 <outputs> | |
20 <data format="txt" name="noncoding" label="${varfile.name}.nc" /> | |
21 <data format="txt" name="coding" label="${varfile.name}.cds" /> | |
22 </outputs> | |
23 <help> | |
24 .. class:: infomark | |
25 | |
26 **What it does** | |
27 | |
28 Annotate a VAR- or DBI-file with **genomic features** and discriminate between **coding** and **non-coding** regions. | |
29 | |
30 - This VAR- or DBI-file has to be generated by either the **SAMVCF_data_parser** or the **Known_variants_finder** gfap utility. | |
31 - The core annotation procedure is mainly performed by the third-party program **annotate_variation.pl** from the ANNOVAR software tools. | |
32 | |
33 .. class:: infomark | |
34 | |
35 **Third-party resources** | |
36 | |
37 - RefSeq: http://www.ncbi.nlm.nih.gov/RefSeq | |
38 - COSMIC: http://www.sanger.ac.uk/genetics/CGP/cosmic | |
39 - ANNOVAR: http://www.openbioinformatics.org/annovar | |
40 | |
41 ---- | |
42 | |
43 **Input .dbi file**:: | |
44 | |
45 #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 | |
46 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 | |
47 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 | |
48 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 | |
49 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 | |
50 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 | |
51 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 | |
52 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 | |
53 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 | |
54 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 | |
55 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 | |
56 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 | |
57 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 | |
58 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 | |
59 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 | |
60 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 | |
61 | |
62 | |
63 ---- | |
64 | |
65 **Output .nc file [non-coding]**:: | |
66 | |
67 #From [chr] to [dbsnp] = DBI file header | |
68 #annot = ig:intergenic; pp:1kb-upstream; 5|3u:UTR; in:intronic; ss:splice; nc:ncRNA | |
69 #ogs = official gene symbol(s) | |
70 #cos = gene listed in cosmic v56 release | |
71 #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 annot ogs cos | |
72 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 nc WASH7P FALSE | |
73 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 nc WASH7P FALSE | |
74 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 pp OR4F5 TRUE | |
75 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 ig na na | |
76 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 ig na na | |
77 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 ig na na | |
78 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 nc FAM41C FALSE | |
79 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 nc FAM41C FALSE | |
80 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 nc FAM41C FALSE | |
81 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 ig na na | |
82 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 ig na na | |
83 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 ig na na | |
84 chr1 846489 846489 T C 0 0 1 1 2 2 1.0000 16 3.33e-01 3.33e-01 3.33e-01 NONE PASS SKIP 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 na na na ig na na | |
85 chr1 866319 866319 G A 0 0 2 1 3 3 1.0000 31 3.33e-01 3.33e-01 3.33e-01 NONE PASS SKIP 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 na na na in SAMD11 TRUE | |
86 chr1 870903 870903 T C 0 0 3 0 3 3 1.0000 65 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 in SAMD11 TRUE | |
87 | |
88 ---- | |
89 | |
90 **Output .cds file [coding]**:: | |
91 | |
92 #From [chr] to [dbsnp] = DBI file header | |
93 #annot = fd:frameshift deletion; fi:frameshift insertion; nd:nonframeshift deletion; ni:nonframeshift insertion; bs:block substitution; ss:synonymous SNV; ns:nonsynonymous SNV; sg:stopgain; sl:stoploss; na:unknown | |
94 #ogs = official gene symbol(s) | |
95 #cos = gene listed in cosmic v56 release | |
96 #mid = RefSeq mRNA identifier(s) from human.protein.gpff r16012012 release | |
97 #pid = RefSeq protein identifier(s) from human.protein.gpff r16012012 release | |
98 #c.x = ATG-based variant descriptor in mRNA | |
99 #p.x = ATG-based variant descriptor in protein | |
100 #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 annot ogs cos mid pid c.x p.x | |
101 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 ss OR4F5 TRUE NM_001005484 NP_001005484 c.A180G p.S60S | |
102 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 ns OR4F5 TRUE NM_001005484 NP_001005484 c.A421G p.T141A | |
103 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 ss OR4F5 TRUE NM_001005484 NP_001005484 c.T807C p.S269S | |
104 chr1 881627 881627 G A 0 0 3 8 11 11 1.0000 88 7.55e-02 3.33e-01 7.55e-02 NONE PASS PASS 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 na na na ss NOC2L TRUE NM_015658 NP_056473 c.C1843T p.L615L | |
105 chr1 887801 887801 A G 0 0 6 0 6 6 1.0000 56 1.04e-02 3.33e-01 1.04e-02 NONE PASS SKIP 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 na na na ss NOC2L TRUE NM_015658 NP_056473 c.T1182C p.T394T | |
106 chr1 888639 888639 T C 0 0 4 9 13 13 1.0000 142 8.89e-02 3.33e-01 8.89e-02 NONE PASS PASS 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 na na na ss NOC2L TRUE NM_015658 NP_056473 c.A918G p.E306E | |
107 chr1 888659 888659 T C 0 0 3 9 12 12 1.0000 146 4.87e-02 3.33e-01 4.87e-02 NONE PASS SKIP 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 na na na ns NOC2L TRUE NM_015658 NP_056473 c.A898G p.I300V | |
108 chr1 897325 897325 G C 0 0 9 11 20 20 1.0000 188 2.75e-01 3.33e-01 2.75e-01 NONE PASS PASS 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 na na na ss KLHL17 TRUE NM_198317 NP_938073 c.G609C p.A203A | |
109 chr1 909238 909238 G C 0 0 3 5 8 8 1.0000 130 2.42e-01 3.33e-01 2.42e-01 NONE PASS SKIP 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 na na na ns PLEKHN1 FALSE NM_032129|NM_001160184 NP_115505|NP_001153656 c.G1460C|c.G1355C p.R487P|p.R452P | |
110 chr1 909242 909242 A G 2 4 1 2 9 3 0.3330 15 1.69e-01 2.29e-01 3.33e-01 NONE PASS SKIP 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 na na na ss PLEKHN1 FALSE NM_032129|NM_001160184 NP_115505|NP_001153656 c.A1464G|c.A1359G p.G488G|p.G453G | |
111 chr1 935222 935222 C A 0 0 0 2 2 2 1.0000 10 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 ns HES4 FALSE NM_001142467 NP_001135939 c.G132T p.R44S | |
112 chr1 949654 949654 A G 0 0 11 9 20 20 1.0000 222 2.75e-01 3.33e-01 2.75e-01 NONE PASS PASS 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 na na na ss ISG15 TRUE NM_005101 NP_005092 c.A294G p.V98V | |
113 chr1 981931 981931 A G 0 0 1 1 2 2 1.0000 36 3.33e-01 3.33e-01 3.33e-01 NONE PASS SKIP 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 na na na ss AGRN TRUE NM_198576 NP_940978 c.A3066G p.S1022S | |
114 chr1 982994 982994 T C 0 0 13 16 29 29 1.0000 146 2.37e-01 3.33e-01 2.37e-01 NONE PASS PASS 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 na na na ss AGRN TRUE NM_198576 NP_940978 c.T3558C p.F1186F | |
115 chr1 1021346 1021346 A G 0 2 2 3 7 5 0.7140 66 1.51e-01 1.67e-01 3.33e-01 NONE PASS SKIP 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 na na na ss C1orf159 FALSE NM_017891 NP_060361 c.T357C p.I119I | |
116 | |
117 ---- | |
118 | |
119 .. class:: infomark | |
120 | |
121 **Feedback**: romain.daveau@curie.fr | |
122 </help> | |
123 </tool> |