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| author | rdaveau |
|---|---|
| date | Fri, 03 Aug 2012 05:50:41 -0400 |
| parents | f753b30013e6 |
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<tool id="gfap_r1.0_allvar_genomic_annotater" name="Map to genomic features"> <description>Annotate variants with ANNOVAR</description> <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> <inputs> <param name="varfile" format="txt" type="data" label="Input VAR or DBI file" /> <param name="buildver" type="select" label="Human reference genome assembly"> <option value="hg19">GRCh37 ie. hg19</option> </param> <param name="refseq_release" type="select" label="human.protein.gpff release"> <option value="r16012012">Jan 16, 2012</option> </param> <param name="cosmic_release" type="select" label="COSMIC db release"> <option value="v56">v56</option> </param> <param name="annovar_release" type="select" label="ANNOVAR db release"> <option value="jan2012">Jan 2012</option> </param> </inputs> <outputs> <data format="txt" name="noncoding" label="${varfile.name}.nc" /> <data format="txt" name="coding" label="${varfile.name}.cds" /> </outputs> <help> .. class:: infomark **What it does** Annotate a VAR- or DBI-file with **genomic features** and discriminate between **coding** and **non-coding** regions. - This VAR- or DBI-file has to be generated by either the **SAMVCF_data_parser** or the **Known_variants_finder** gfap utility. - The core annotation procedure is mainly performed by the third-party program **annotate_variation.pl** from the ANNOVAR software tools. .. class:: infomark **Third-party resources** - RefSeq: http://www.ncbi.nlm.nih.gov/RefSeq - COSMIC: http://www.sanger.ac.uk/genetics/CGP/cosmic - ANNOVAR: http://www.openbioinformatics.org/annovar ---- **Input .dbi file**:: #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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 ---- **Output .nc file [non-coding]**:: #From [chr] to [dbsnp] = DBI file header #annot = ig:intergenic; pp:1kb-upstream; 5|3u:UTR; in:intronic; ss:splice; nc:ncRNA #ogs = official gene symbol(s) #cos = gene listed in cosmic v56 release #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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 ---- **Output .cds file [coding]**:: #From [chr] to [dbsnp] = DBI file header #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 #ogs = official gene symbol(s) #cos = gene listed in cosmic v56 release #mid = RefSeq mRNA identifier(s) from human.protein.gpff r16012012 release #pid = RefSeq protein identifier(s) from human.protein.gpff r16012012 release #c.x = ATG-based variant descriptor in mRNA #p.x = ATG-based variant descriptor in protein #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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 ---- .. class:: infomark **Feedback**: romain.daveau@curie.fr </help> </tool>