about VRanges and filtering somatic variants
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Bogdan ▴ 640
@bogdan-2367
Last seen 3 days ago
Palo Alto, CA, USA

Dear all,

i would appreciate please your suggestions on the proper use of Vranges. I have a vcf file with somatic variants that looks in the following way (below). I would like to select/filter only the variants that have an AD > 5 and AF > 0.05 in the TUMOR sample (the vcf file was generated by MUTECT2). 

The code below works :

svp <- ScanVcfParam(geno=c("AD","AF"), samples="TUMOR")

vcf2 <- readVcfAsVRanges("AML_expanded.vcf", "hg38", svp)

however, why the other piece of code (below) does not work properly, when I import both fields for NORMAL and TUMOR ? Thank you very much !

svp <- ScanVcfParam(info="DP", geno=c("AD","AF"), samples=c("NORMAL","TUMOR"))

A few lines in the VCF file look in the following way :

#CHROM    POS    ID    REF    ALT    QUAL    FILTER    INFO    FORMAT    NORMAL    TUMOR
chr1    108044    chr1:108044_C/G    C    G    .    PASS    BaseCounts=0,45,5,0;ECNT=1;FS=8.486;GC=39.6;HCNT=1;HRun=0;LowMQ=0,0.06,50;NLOD=2.41;SOR=1.874;TLOD=7.89;VariantType=SNP    GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1    0/0:8,0:0:0:0:.:238:6:2    0/1:38,5:0.116:3:2:0.4:1113:19:19
chr1    123100    chr1:123100_A/ATG    A    ATG    .    PASS    BaseCounts=65,0,3,0;ECNT=1;GC=27.72;HCNT=1;HRun=0;LowMQ=0,0.0441,68;NLOD=5.06;RPA=5,6;RU=TG;STR;TLOD=11.79;VariantType=INSERTION.NumRepetitions_5.EventLength_2.RepeatExpansion_TG    GT:AD:AF:ALT_F1R2:ALT_F2R1:QSS:REF_F1R2:REF_F2R1    0/0:32,4:0.058:0:0:903:17:13    0/1:31,13:0.173:2:1:885:13:18
chr1    187017    chr1:187017_G/C    G    C    .    PASS    BaseCounts=0,10,161,0;ECNT=1;FS=4.83;GC=29.7;HCNT=1;HRun=0;LowMQ=0,0.0819,171;NLOD=28.89;SOR=1.59;TLOD=7.71;VariantType=SNP    GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1    0/0:101,0:0:0:0:.:3012:50:51    0/1:133,7:0.05:3:4:0.429:3830:59:74

 

vranges vcf to vranges • 856 views
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#CHROM    POS    ID    REF    ALT    QUAL    FILTER    INFO    FORMAT    NORMAL    TUMOR
chr1    108044    chr1:108044_C/G    C    G    .    PASS    BaseCounts=0,45,5,0;ECNT=1;FS=8.486;GC=39.6;HCNT=1;HRun=0;LowMQ=0,0.06,50;NLOD=2.41;SOR=1.874;TLOD=7.89;VariantType=SNP    GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1    0/0:8,0:0:0:0:.:238:6:2    0/1:38,5:0.116:3:2:0.4:1113:19:19
 

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What does 'does not work properly' mean?

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Hi Martin, thank you for your question : I have re-run the R code, and excepting < 10 variants in the vcf file, everything else look fine, and the variants are printed in the output file. Thanks a lot, and happy weekend !

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