Open syansanofi opened 3 years ago
Is it possible to merge these two tools into a single one? For example:
picard MarkDuplicates REMOVE_DUPLICATES=true
can be used.
Is there another situation where we need a separate samtools call to mark the duplicate?
Additionally CREATE_INDEX=true can also be used to replace the indexing of duplicate reads
picard MarkDuplicates REMOVE_DUPLICATES=true --CREATE_INDEX=true
@syansanofi Yes, it's possible. We apply PicardRemoveDuplicate if rmdup flag is on or these are scRnaExpression_Fastq or capture or WGS workflows. Should we preserve this logic?
rmdup
scRnaExpression_Fastq
capture
WGS
Is it possible to merge these two tools into a single one? For example:
picard MarkDuplicates REMOVE_DUPLICATES=true
can be used.
Is there another situation where we need a separate samtools call to mark the duplicate?
Additionally CREATE_INDEX=true can also be used to replace the indexing of duplicate reads
picard MarkDuplicates REMOVE_DUPLICATES=true --CREATE_INDEX=true