Question: Some clarification on Strelka output
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gravatar for A
4 days ago by
A3.7k
A3.7k wrote:

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

wgs vaf strelka vcf • 81 views
ADD COMMENTlink written 4 days ago by A3.7k
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