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.
-
The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...07-08-2024, 03:19 PM