callvariants.sh & marked duplicated reads
BBMap short read aligner, and other bioinformatic tools.
Brought to you by:
brian-jgi
Menu
▾
▴
#42 callvariants.sh & marked duplicated reads
Dear Brian,
I want to use MarkDuplicates from Picardtools to mark duplicated reads from sorted BAM files and I was wondering whether callvariants.sh from BBtools will recognize these reads that have been marked as duplicates? Or would you suggest to remove duplicated reads completely prior to the variant calling step?