I was wondering if trimming 3' end of the reads for somatic variants calling could have positive effects for the called results.
I have tested a sample which is split into 2 sets and sequenced at same time. And then used these two sequencing results to go through same somatic variant calling pipeline.
The result was too different.
So I tried trimming 3' end of the reads for about 20bp and then went through it again. Surprisingly, the results were almost the same..
At the analysis process which I didn't trim end of the reads, quality filtering such as Q30 bp and mapping quality filtering were done, too.
I'm curious if bp QC and mapping QC filtering weren't effective and why trimming 3' end of the reads seemed to work.
Any advise will be very grateful!