Some clarification on Strelka output

Question

[zizigolu]

Hi

In this link

https://github.com/Illumina/strelka/blob/v2.9.x/docs/userGuide/README.md#somatic

The somatic allele frequency estimate in the tumor sample is not directly available in the VCF output

But I am seeing somatic allele frequency here in Strelka vcf for SNVs

chrM    1097    .   G   A   .   PASS    Depth=9609;DistanceToAlignmentEnd=26.06;DistanceToAlignmentEndMAD=13.00;DistanceToAlignmentEndMedian=26.00;HomopolymerLength=3;LowMapQual=6.240e-03;MMQSDiff=34.83;MapQualDiff=-5.398e-01;MapQualDiffMedian=0.00;NT=ref;QSS=2663;QSS_NT=1316;ReadCount=8967;ReadCountControl=2758;Repeat=4;SGT=GG->AG;SNVCluster10=0;SNVCluster100=0;SNVCluster20=0;SNVCluster5=0;SNVCluster50=0;SOMATIC;StrandBias=0.435;TQSS=1;TQSS_NT=1;VariantAlleleCount=1775;VariantAlleleCountControl=1;VariantAlleleFrequency=0.198;VariantBaseQual=34.78;VariantBaseQualMedian=37.00;VariantMMQS=36.12;VariantMapQual=43.15;VariantMapQualMedian=40.00;VariantStrandBias=0.427 DP:FDP:SDP:SUBDP:AU:CU:GU:TU    2860:24:0:0:1,1:5,10:2828,2854:2,3  9531:96:0:0:1892,1917:48,65:7494,7554:1,8

Which is 0.198 for this position, then why they say we could calculate that ourselves

[parvathi.sudha]

Hi,

Can you please tell which command you used here? When I performed Strelka analysis, the vcf files don't show the allele frequency values. I am using strelka-2.9.2.

Thanks

Parvathi.

[zizigolu]

Strelka itself does not calculate and show variant allele frequency You have to calculate that from INFO column part like read depth for mutant and wild type

[parvathi.sudha]

Hi,

Any idea on which R package to use for calculating variant allele frequency for tumor and normal samples? vcf file version v4.1

Thanks Parvathi

[zizigolu]

Hi

I have script to calculate that

Separate scripts for SNVs and INDELs

Tomorrow I will locate that and share with you

[parvathi.sudha]

That will great. I appreciate your help. Thank you

[zizigolu]

This is for SNVs

https://www.dropbox.com/s/a4opysn734ua1yp/SNV.parsing?dl=0

This for INDELs

https://www.dropbox.com/s/sz1s4wrqtmb54s8/Reworked_IZADI_indel_vcf_parasing.sh.download.zip?dl=0

[ATpoint]

The Strelka manual explains in detail how to calculate AFs from VCF files. Be sure to read this and validate that this is in line with the suggested code from these Dropboxes. The first link talks about amino acids so this at least has nothing to do with AFs from Strelka output.

[zizigolu]

@ATpoint thank you for checking, I edited the first link to the right script

My bad in adding the right one

Actually I am nothing in coding so this script come from my supervisors working on Strelka .vcf

[parvathi.sudha]

Thank you for the script. It was little different from what I was looking.

Using vcftools, I extracted the AD (Read depth for each allele) values of normal and tumor for calculating the vaf for each variant.

Code: vcftools --vcf variants.vcf --extract-FORMAT-info AD

Thank you for the help.

[ATpoint]

Please note: