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If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
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Depth with and without Soft-Clipping

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?
Thanks!
Tagged:
Answers
@ccnn
Hi,
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.
-Sheila
@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
?@ccnn
Hi,
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
-Sheila