Hello,
how does sambamba depth deals with secondary and supplementary alignments in a sam/bam file?
I know samtools depth ignores them, what about sambamba? From the documentation, it's said that the default filter "the default value is 'mapping_quality > 0 and not duplicate and not failed_quality_control'"
does it mean it takes into account the secondary and supplementary alignments?
Also, bwa mem (which is my usual mapper), can report a mapping_quality of 0 if it can't decide between different alignments, am I right to understand that then sambamba will ignore those alignments in the computation of the coverage?
Hello, how does sambamba depth deals with secondary and supplementary alignments in a sam/bam file? I know samtools depth ignores them, what about sambamba? From the documentation, it's said that the default filter "the default value is 'mapping_quality > 0 and not duplicate and not failed_quality_control'" does it mean it takes into account the secondary and supplementary alignments? Also, bwa mem (which is my usual mapper), can report a mapping_quality of 0 if it can't decide between different alignments, am I right to understand that then sambamba will ignore those alignments in the computation of the coverage?
Thanks a lot.