How to generate a bam file with reads of only a certain length?
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2.2 years ago
Hrishikesh • 0

I have certain bam files which have reads of different size. I wish to create another bam file from it which has reads smaller than a certain length N. I should be able to run samtools stats and idxstats like commands on it. Is there a way to do it?

samtools • 817 views
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You can use samtools view -h myfile.bam | awk 'length($10) > 30 || $1 ~ /^@/' | samtools view -bS - > out.bam from Ashutosh Pandey answer available here Filtration Of Reads With Length Lower Than 30 From Bam

Where 30 is the minimum length

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Hey, can range be used in this case? Like if I want it to be 20 < 'length($10) < 30? Or must I perform these actions separately? Much thanks for your previous answer

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Sure;
samtools view -h myfile.bam | awk '(length($10) > 20 && length($10) < 30) || $1 ~ /^@/' | samtools view -bS - > out.bam

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2.2 years ago
samtools view -e 'length(seq)<100'  -O BAM -o out.bam in.bam
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