Question

extracting reads from bam file

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6.5 years ago

KVC_bioinfo ▴ 590

Hello all,

I am trying to extract the reads falling into the particular region from a bam file. I am using the following command:

samtools view -b out.bam "chr10:regionstart-regionend" > region.bam

When I run this command I only get one read into the output. However, I can see many reads mapping in that particular region when I visualize the alignment in IGV.

Could someone help me identify what am I doing wrong?

Thank you in advance

bam fasta samtools • 2.9k views

ADD COMMENT • link 6.5 years ago by KVC_bioinfo ▴ 590

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what is the version of samtools, did you try to re-index the bam ?

ADD REPLY • link 6.5 years ago by Pierre Lindenbaum 161k

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Program: samtools (Tools for alignments in the SAM format) Version: 0.1.19-44428cd

No I did not re-index it.

ADD REPLY • link 6.5 years ago by KVC_bioinfo ▴ 590

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try to re-index; Use a newer version of samtools (I'm not sure 0.1.19 is able to handle supplementary alignments)

ADD REPLY • link 6.5 years ago by Pierre Lindenbaum 161k

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As pciifen said, region format is chr:start-stop, like "chr3:1000-2000"

ADD REPLY • link 6.5 years ago by kumajis • 0

score 2 · Answer 1 · 2017-11-21

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6.5 years ago

pcliften ▴ 20

Are you really using a colon ":" between your regionstart and regionend numbers instead of a dash "-"?

ADD COMMENT • link 6.5 years ago by pcliften ▴ 20

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Sorry, its '-'

I made a typo there in thepost. I will correct it.

ADD REPLY • link 6.5 years ago by KVC_bioinfo ▴ 590