varscan - how to calculate MinMMQSdiff
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4.0 years ago
reany ▴ 50

There is a variant result from varscan fpfilter using default parameter like below :

17 7579362 . AACC A . MinMMQSdiff DP=473;SOMATIC;SS=2;SSC=255;GPV=1E0;SPV=6.8578E-82 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:89:89:0:0%:68,21,0,0 1/1:.:384:14:370:96.35%:5,9,244,126

the used bam-readcount result is

17 7579363 A 405 =:0:0.00:0.00:0.00:0:0:0.00:0.00:0.00:0:0.00:0.00:0.00 A:0:0.00:0.00:0.00:0:0:0.00:0.00:0.00:0:0.00:0.00:0.00 C:0:0.00:0.00:0.00:0:0:0.00:0.00:0.00:0:0.00:0.00:0.00 G:1:60.00:32.00:0.00:1:0:0.01:0.01:32.00:1:0.01:135.00:0.01 T:0:0.00:0.00:0.00:0:0:0.00:0.00:0.00:0:0.00:0.00:0.00 N:0:0.00:0.00:0.00:0:0:0.00:0.00:0.00:0:0.00:0.00:0.00 -ACC:404:60.00:0.00:0.00:243:161:0.50:0.02:8.15:243:0.48:134.91:0.46

I think the MMQSdiff=var-ref=8.15-0=8.15 is greater than 0 (the default --min-mmqs-diff value is 0). Why the locus was still marked as MinMMQSdiff ?

varscan bam-readcount MinMMQSdiff • 681 views
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