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Possible To Convert Bam To Bam?

Is it possible to convert bam to bam? I have bam produced by default BWA; but I may also need bam filtered by tossing out those with mapping quality< 20. We can convert sam to bam with a quality cut-off as 20, but storage of sam file is painful (simply too large). So just wondering if I can convert default bam to quality-control bam, so that I only need to store bam file in my system.

thx

bwa bam samtools
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updated by Rm Rm • written by Bioscientist Bioscientist

3 answers

samtools view -b -q 20 in.bam > out.bam

This will filter any alignments with a mapping quality < 20 from in.bam to out.bam

• 1 views • link
written by Gww Gww

You can do this with [?]samtools[?]:

Samtools view has these options:

-b        Output in the BAM format.
-q INT    Skip alignments with MAPQ smaller than INT [0]
• 1 views • link
written by Damian Kao Damian Kao

samtools view -q 20 -b inputbam > outputq20.bam

• 2 views • link
written by Rm Rm

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