samtools view region and include duplicate reads
Hello all,
I have paired end whole genome NGS data. I'm trying to extract reads and their mates.
ID_A is the ID of a mate pair aligning to chr12. If I use:
samtools view whole_genome.bam | grep ID_A
it returns both reads. However if I use:
samtools view whole_genome.bam chr12 | grep ID_A
it only returns the read which is not marked as a PCR duplicate. Is there a flag which will return PCR duplicates when viewing a region.
Thanks in advance for your help!
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hum ..
grepcannot change the behavior ofsamtoolsin that context.Hmm yes, the question is more how to change the output of samtools view when a region is added.
When using samtools view with a region given, reads marked as duplicates do not show but their mate does. I want to view these duplicate reads when a region is given.
Appreciate your time!
I still don't understand. Duplicates should be mapped at the same place.
Please show the SAM entry of the respective read(s), this is more straight forward to interpret than textual descriptions.