VEP for cancer annotation using COSMIC
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Entering edit mode
9 months ago
yussab ▴ 50

Dear all,

I'm struggling in finding how to obtain information about COSMIC database after I annotate a vcf using VEP. The command that I used is:

vep -i Mutect2_unfiltered_10643_vs_2434.vcf.gz
-o Mutect2_unfiltered_10643_vs_2434_VEP.ann.vcf
--assembly GRCh38
--species homo_sapiens
--offline --cache --cache_version 99
--dir_cache /.vep --everything --filter_common
--fork 4 --format vcf --per_gene --stats_file Mutect2_unfiltered_10643_vs_2434_VEP.summary.html
--total_length --vcf

I get back a vcf annotated file, but I'm not able to find any COSMIC information. Maybe there is a way to filter only for COSMIC??

Thank you in advance, Youssef

VEP COSMIC Cancer • 852 views
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Entering edit mode
9 months ago
Emily 23k

The COSMIC variants should appear listed as SOMATIC under the co-located variants. You may find that your --filter_common option is excluding some COSMIC variants. I would recommend running without this then using the VEP filter tool with --filter "SOMATIC" to find COSMIC variants.

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Thank you Emily, I'll try and let you know how it worked! :)

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Dear Emily, I filtered my vcf file using this command:

filter_vep -i Mutect2_filtered_VEP.ann.vcf.gz -o out_filtered_SOMATIC.vcf --filter "SOMATIC"

I obtain the result in the table, however I'm still confused on how to interpret these vcf file.

**filtering_status=These calls have been filtered by FilterMutectCalls to label false positives with a list of failed filters and true positive s with PASS.

**normal_sample=2682

**source=FilterMutectCalls

**source=Mutect2

**tumor_sample=10643

**VEP="v99" time="2021-02-10 15:29:22" cache="/hpcshare/genomics/sarek_analyses/work/b6/54109e400c87375cc7a5d169ec2bc2/vep_cache/homo_sapiens/99_GRCh38" ensembl-funcgen=99.0832337 ensembl=99.d3e7d31 ensembl-variation=99.642e1cd ensembl-io=99.441b05b 1000genomes="phase3" COSMIC="90" ClinVar="201909" ESP="V2-SSA137" HGMD-PUBLIC="20184" assembly="GRCh38.p13" dbSNP="153" gencode="GENCODE 33" genebuild="2014-07" gnomAD="r2.1" polyphen="2.2.2" regbuild="1.0" sift="sift5.2.2"

**INFO=-ID=CSQ,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|DISTANCE|STRAND|FLAGS|VARIANT_CLASS|SYMBOL_SOURCE|HGNC_ID|CANONICAL|MANE|TSL|APPRIS|CCDS|ENSP|SWISSPROT|TREMBL|UNIPARC|GENE_PHENO|SIFT|PolyPhen|DOMAINS|miRNA|HGVS_OFFSET|AF|AFR_AF|AMR_AF|EAS_AF|EUR_AF|SAS_AF|AA_AF|EA_AF|gnomAD_AF|gnomAD_AFR_AF|gnomAD_AMR_AF|gnomAD_ASJ_AF|gnomAD_EAS_AF|gnomAD_FIN_AF|gnomAD_NFE_AF|gnomAD_OTH_AF|gnomAD_SAS_AF|MAX_AF|MAX_AF_POPS|CLIN_SIG|SOMATIC|PHENO|PUBMED|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE"-

*CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 10643 2682

chr1 16534 . C T . map_qual;normal_artifact;panel_of_normals AS_FilterStatus=map_qual;AS_SB_TABLE=38,71|1,12;DP=126;ECNT=2;GERMQ=29;MBQ=32,30;MFRL=305,438;MMQ=23,23;MPOS=29;NALOD=-9.266e+00;NLOD=7.26;PON;POPAF=0.305;TLOD=9.60;CSQ=T|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene||||||||||rs15642|2864|1||SNV|HGNC|HGNC:37102||||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript||||||||||rs15642|2125|1||SNV|HGNC|HGNC:37102|YES||1|||||||||||||||||||||||||||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene||8/10|ENST00000488147.1:n.1067+73G>A|||||||rs15642||-1||SNV|HGNC|HGNC:38034|YES|||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|MIR6859-1|ENSG00000278267|Transcript|ENST00000619216|miRNA||||||||||rs15642|835|1||SNV|HGNC|HGNC:50039|YES|||||||||||||||||||||||||||||||||||||||||,T|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000344266|CTCF_binding_site||||||||||rs15642||||SNV|||||||||||||||||||||||||||||||||||||||||||| GT:AD:AF:DP:F1R2:F2R1:SB 0/1:8,4:0.416:12:5,3:3,1:3,5,0,4 0/0:101,9:0.090:110:53,5:46,3:35,66,1,8

(I changed #/< with */- for formatting issues)

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Entering edit mode
7 weeks ago

if you want cosmic annotation, you should use the option --custom

http://asia.ensembl.org/info/docs/tools/vep/script/vep_cache.html#gfftypes
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7 weeks ago

Run VEP annotation

vep -i in.vcf -o OUT.TXT --fasta /hg19.fasta --assembly GRCh37 --offline --cache --dir_cache /$HOME/.vep --everything --fork 4 --format vcf --per_gene --stats_file Mutect2_unfiltered_10643_vs_2434_VEP.summary.html --total_length –vcf

Output will look like this

IMPACT=MODERATE;STRAND=-1;VARIANT_CLASS=substitution;SYMBOL=KRAS;SYMBOL_SOURCE=HGNC;HGNC_ID=6407;BIOTYPE=protein_coding;CANONICAL=YES;CCDS=CCDS8703.1;ENSP=ENSP00000256078;SWISSPROT=RASK_HUMAN;TREMBL=Q9UM97_HUMAN,Q71SP6_HUMAN,P78460_HUMAN,L7RSL8_HUMAN,I1SRC5_HUMAN;UNIPARC=UPI0000133132;GENE_PHENO=1;SIFT=deleterious(0);PolyPhen=probably_damaging(0.987);EXON=2/6;DOMAINS=Gene3D:3.40.50.300,Pfam:PF00071,Prints:PR00449,PROSITE_profiles:PS51421,PANTHER:PTHR24070,PANTHER:PTHR24070:SF186,SMART:SM00173,SMART:SM00174,SMART:SM00175,SMART:SM00176,Superfamily:SSF52540,TIGRFAM:TIGR00231,Low_complexity_(Seg):seg;SOMATIC=1,1,1,1,1,1,1;PHENO=1,1,1,1,1,1,1

Then filter

filter_vep -i OUT.TXT -o out_filtered.txt -filter "SOMATIC"

I hope that works

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