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Dear all,
for filtering a VCF file based on various criteria (Allelic Depth or Allelic Frequency, etc), which libraries would in BioC you recommend to use ? thank you ;) !
-- bogdan
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VariantAnnotation::filterVcf() (and vignette) would be one candidate; TVTB also implements filters, with an extensive vignette. HelloRanges translates bedtools queries to GRanges functions, which can be used on VCF objects from VariantAnnotation.
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Dear Martin, thank you and happy and fruitful new year ! yes, I have started with VariantAnnotation(); and I may have some little questions along the way ;) thanks for your help !
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Hi Martin, please when you have a minute, may I ask you for a suggestion : shall I have a VCF file as it is described below, what would be the fastest way to select only the variants with AD > 5, and AF > 0.05 ? thanks !
| #CHROM | POS | ID | REF | ALT | QUAL | FILTER | INFO | FORMAT | TUMOR | NORMAL |
| chr1 | 146139995 | 0 | T | C | 0 | PASS | BaseCounts=1,5,0,38;ECNT=1;FS=4.639;GC=52.48;HCNT=2;HRun=0;LowMQ=0.0000,0.0682,44;MAX_ED=.;MIN_ED=.;NLOD=7.78;SOR=1.916;TLOD=7.51;VariantType=SNP;ANNOVAR_DATE=2016-02-01;Func.refGene=exonic;Gene.refGene=NBPF10;GeneDetail.refGene=.;ExonicFunc.refGene=nonsynonymous_SNV;AAChange.refGene=NBPF10:NM_001039703:exon5:c.A592G:p.K198E,NBPF10:NM_001302371:exon5:c.A592G:p.K198E;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=4.51;FATHMM_pred=T;PROVEAN_score=.;PROVEAN_pred=.;VEST3_score=0.26;CADD_raw=0.353;CADD_phred=6.192;DANN_score=0.130;fathmm-MKL_coding_score=0.000;fathmm-MKL_coding_pred=N;MetaSVM_score=-0.961;MetaSVM_pred=T;MetaLR_score=0.008;MetaLR_pred=T;integrated_fitCons_score=0.693;integrated_confidence_value=0;GERP�_RS=-0.47;phyloP7way_vertebrate=-1.190;phyloP20way_mammalian=-1.003;phastCons7way_vertebrate=0.002;phastCons20way_mammalian=0.004;SiPhy_29way_logOdds=3.32;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;HRC_AF=.;HRC_AC=.;HRC_AN=.;HRC_non1000G_AF=.;HRC_non1000G_AC=.;HRC_non1000G_AN=.;esp6500siv2_ea=.;esp6500siv2_aa=.;esp6500siv2_all=.;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;Kaviar_AF=.;Kaviar_AC=.;Kaviar_AN=.;avsnp144=.;nci60=.;clinvar_20150629=.;ALLELE_END | GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1 | 0/1:31,5:0.139:2:3:0.400:904,143:18:13 | 0/0:26,0:0.00:0:0:.:759,0:10:16 |
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Thank you Martin, will open a new question ;)