I'm using VarScan.v2.2.11.
The problem I'm reporting here is something about VarScan's parameter --min-avg-qual when using command mpileup2indel. I'm setting it to be default, which is 15.
In the input pileup file:
CHROMOSOME_I 221154 g 42 .,,,,,,,+1c,+1c,,+1c,+1c,+1c,+1c,+1c,+1c,+1c,+1c,+1c,+1c,+1c.+1C,+1c.+1C,+1c,+1c,+1c,+1c.+1C.+1C,+1c,+1c,+1c.+1C,+1c,+1c,+1c.+1C.+1C.+1C.+1C.+1C 1C?C<FFFFDHJEAJDJIJG<JJG'GIDIJBD9JDDDG?FDF
The corresponding output:
CHROMOSOME_I 221154 G +C */+C:41:8:34:45.33%:4.4044E-13 Pass:11:30:10:24:1E0 0 1 0 0 */+C:41:8:34:45.33%:4.4044E-13
The red colored part of the input won't get passed the --min-avg-qual filteration, because it's base quality is less than 15. The prblem is that in the output, we see the Cov=41 (which is correct), Reads1=8 (which is also correct), but Reads2=34 (which should be 33, because one of the insertion has mapping quality less than 15).
Anyone has a similar problem like me? Could anyone help? I think this might be a bug of VarScan.
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