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Uncorrect Strand Bias due to Downsampling (HaplotypeCaller)
Hi GATK team,
Again thanks a lot for the wonderful tools you're offering to the community.
I have recently switched from UnifiedGenotyper to Haplotype Caller (1 sample at a time, DNASeq). I was planning to use the same hard filtering procedure that I was using previously, including the filter of the variants with FS > 60.
However I am facing an issue probably due to the downsampling done by HC.
I should have 5000 reads, but DP is around 500/600 which I understood is due to downsampling (even with -dt NONE). I did understand that it does not impact in the calling itself. However it is annoying me for 2 reasons
1) Calculating frequency of the variant using the AD field is not correct (not based on all reads)
2) I get variants with FS >60 whereas when you look at the entire set of reads, there is absolutely no strand bias.
Example with this variant
chr17 41245466 rs1799949 G A 7441.77 STRAND_BIAS; AC=1;AF=0.500;AN=2;BaseQRankSum=7.576;DB;DP=1042;FS=63.090;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.666;QD=7.14;ReadPosRankSum=-11.896;SOR=5.810 GT:AD:GQ:PL:SB 0/1:575,258:99:7470,0,21182:424,151,254,4
When I observe all reads I have the following counts, well shared on the + and - strands
Allele G : 1389 (874+, 515-)
Allele A : 1445 (886+, 559-)
Could you please tell me how to avoid such an issue ? (By the way, this variant is a true one and should not be filtered out).
Thanks a lot.