Question

How to extract alignments with 0 mismatch from sam or bam file by using samtools?

0

Entering edit mode

3.4 years ago

khanhlpbao • 0

I have a single-ended sam files generated from bwa with default settings for NIPT calculation. How can I extract a sam or bam files that contains only alignments that have 0 mismatch by using samtools?

bam samtools sam • 3.4k views

ADD COMMENT • link updated 17 months ago by Hien • 0 • written 3.4 years ago by khanhlpbao • 0

score 0 · Answer 1 · 2021-06-02

0

Entering edit mode

3.4 years ago

badribio ▴ 290

You could use this samtools view -h bwa.bam | grep "NM:i:0" | samtools view -O BAM -o bwa.filtered.bam

ADD COMMENT • link 3.4 years ago by badribio ▴ 290

0

Entering edit mode

Thanks, can I replace bwa.bam with bwa.sam? Or I need to convert it to bam first?

ADD REPLY • link 3.4 years ago by khanhlpbao • 0

0

Entering edit mode

this is wrong, the last command is trying to read a file bwa.filtered.bam. You want .. | samtools view -O BAM -o bwa.filtered.bam

ADD REPLY • link 3.4 years ago by Pierre Lindenbaum 164k

0

Entering edit mode

Hi, by somehow it shows error: no header when type together but worked when I type them separately

ADD REPLY • link 3.4 years ago by khanhlpbao • 0

score 0 · Answer 2 · 2021-06-02

0

Entering edit mode

3.4 years ago

Pierre Lindenbaum 164k

samtools view -e '[NM]==0' -O BAM -o out.bam   in.bam

requires a recent version of samtools.

ADD COMMENT • link 3.4 years ago by Pierre Lindenbaum 164k

0

Entering edit mode

Oops those were from my notes dates 5 years back my bad. edited my answer.

ADD REPLY • link 3.4 years ago by badribio ▴ 290