Question

Tool for BAM coverage without the soft clipping base

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7.5 years ago

nayshool ▴ 20

Hi everyone,

I am looking for a software/script which calculate the mean coverage of an area without the soft clipping bases. It's exclude the soft/hard clipping bases and leave only the true annotated bases in the calculation.

thank you

BAM coverage softclipping • 2.7k views

ADD COMMENT • link updated 7.5 years ago by Pierre Lindenbaum 164k • written 7.5 years ago by nayshool ▴ 20

score 0 · Answer 1 · 2017-05-29

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7.5 years ago

Devon Ryan 104k

Almost anything that produces coverage metrics will do what you're describing. As an example, you can use bamCoverage or multiBamSummary from deepTools to do this, though other common choices would be bedtools or even featureCounts.

ADD COMMENT • link 7.5 years ago by Devon Ryan 104k

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I don't want to count the soft clipping reads. Are those software will not count them?

ADD REPLY • link 7.5 years ago by nayshool ▴ 20

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Correct, none of those (or even samtools view -c) will count soft-clipped portions of reads.

ADD REPLY • link 7.5 years ago by Devon Ryan 104k

score 0 · Answer 2 · 2017-05-29

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7.5 years ago

Pierre Lindenbaum 164k

GATK depthofcoverage: https://software.broadinstitute.org/gatk/gatkdocs/3.7-0/org_broadinstitute_gatk_tools_walkers_coverage_DepthOfCoverage.php

In most (all?) tools the clipping section is ignored.

ADD COMMENT • link 7.5 years ago by Pierre Lindenbaum 164k