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Depth with and without Soft-Clipping

ccnnccnn Member
edited May 2018 in Ask the GATK team

Hi guys,

I'm trying to use GATK3 (since v4 doesn't have the DepthOfCoverage tool yet) to calculate the depth of coverage across some WGS BAM files, with and with out soft clipping.

Currently, I'm using the following the following

#calculate depth, exclude soft-clipped bases
java -Xmx${mem}g -jar $jar -mbq 0 -mmq 0 -L ${bed} -o $out/${bamName}.doc -I $bam  -T DepthOfCoverage -R $ref

#calculate depth, include soft-clipped bases
java  -Xmx${mem}g -jar $jar -T ClipReads -l INFO -I $bam -o $bam.noclip.bam -R $ref -CR REVERT_SOFTCLIPPED_BASES -os clip.stats 2>> err.sc >> out.sc
java  -Xmx${mem}g -jar $jar -mbq 0 -mmq 0 -L $bed -o $out/${bamName}.noclip.bam.doc -I $bam.noclip.bam  -T DepthOfCoverage -R $ref

Basically, what I'm asking GATK to do is: 1) traverse the original BAM file and calculate the depth; 2) convert this original BAM file into a new BAM file with no soft clipping; 3) traverse this new BAM file and calculate the depth.

This is a computationally intensive process; it takes both large amounts of time and memory. And I'm wondering if there's a more efficient way to do it?



  • SheilaSheila Broad InstituteMember, Broadie ✭✭✭✭✭
    edited May 2018


    I don't think there is an easier way to do it, unfortunately.
    You may want use some outside tools that do consider soft clips when calculating coverage.


  • ccnnccnn Member
    edited May 2018

    @Sheila thanks for your quick response. Could you point me toward some of these tools? I'm assuming these tools don't also report the coverage without soft-clipping, right?—meaning I could use them only as a substitute for my current method for #calculate depth, include soft-clipped bases?

  • SheilaSheila Broad InstituteMember, Broadie ✭✭✭✭✭


    I think Qualimap has a way to output the number of hard and soft clipped reads. I did a quick google search and people recommend bedtools on biostars. You may also try asking on biostars. Let us know what you use/find :smile:


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