Hello,
I have some question concerning samtools bedcov to which I didn't found answers until now.
1. Does bedcov ignore reads marked as PCR/optical duplicates when calculating the coverage?
2. It seems that bedcov needs the index bam file. Right?
So I have a batch of bam files in which pcr duplicates are not flagged. I need to run PicardTools MarkDuplicates on them. I would like to pipe the output directly to bedcov, but because the output have no index it doesn't work. Is there a way to pipe to bedcov without creating intermediate files?
Thanks for your help.
fin swimmer
I have some question concerning samtools bedcov to which I didn't found answers until now.
1. Does bedcov ignore reads marked as PCR/optical duplicates when calculating the coverage?
2. It seems that bedcov needs the index bam file. Right?
So I have a batch of bam files in which pcr duplicates are not flagged. I need to run PicardTools MarkDuplicates on them. I would like to pipe the output directly to bedcov, but because the output have no index it doesn't work. Is there a way to pipe to bedcov without creating intermediate files?
Thanks for your help.
fin swimmer
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