Question

Distinguish BAM vs BAMPE format

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7.7 years ago

cpak1981 ▴ 140

How can I tell if my BAM file is in BAM(SE) or BAMPE format? Does samtools have a command to help with this?

BAM BAMPE BWA • 3.6k views

ADD COMMENT • link 7.7 years ago by cpak1981 ▴ 140

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Thanks Pierre! Appreciate your time

ADD REPLY • link 7.7 years ago by cpak1981 ▴ 140

score 1 · Answer 1 · 2017-03-07

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7.7 years ago

Pierre Lindenbaum 164k

you can use the samflag n°1 https://broadinstitute.github.io/picard/explain-flags.html and samtools view with option -f and/or -F to extract the reads paired or not paired.

ADD COMMENT • link 7.7 years ago by Pierre Lindenbaum 164k