Dear samtools team and colleagues,
I have several questions about the use of samtools rmdup utility. They are
partially covered on forums, but I'd like to clarify some points:
1) Am I right that if I have a BAM file that contains both paired-end and
single-end reads, I can't dedup them simultaneously in one run of rmdup?
Should I first run samtools rmdup with no additional options to dedup
paired-end reads and then run samtools rmdup -s on the result obtained to
get single-end reads deduped?
2) Does it matter if paired-end reads were processed with Trimmomatic
before mapping, so they can have different lengths due to a low-quality
ends trimming?
Best regards,
Svyatoslav
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