interval list for CNV analysis of samples being sequence using target panel platform
I have samples being sequenced using a commercial target panel platform. If I want to do somatic CNV analysis, for the interval list, should I follow the protocol as WGS or exom? I did not have the bed file of the targets. I only know the gene name for those targets.
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Unless you have your targets available it will be a problem to compare against the PON using the same targets. One particular solution could be to generate these target regions using an older version of the gatk.
GATK 3 has the command called CallableLoci. You may tune your paremeters to export call callable regions with certain depth and mapping quality as a BED file then you may fine tune all the regions generated to come up with a refined set of target regions to be used by GATK Somatic CNV workflow.
I hope this helps.
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thank you for helping and sorry for late response.
I finally get the bed files of the panel design. In order to run the pipeline correctly, should I subset the interval list with my target region?
gatk-master/ref/intervals_wgs_coverage_regions.hg38.interval_list
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You don't need to use the whole genome regions for that. You can convert you bed file to an interval_list and perform preprocessing such as GC content annotation etc. Then you can use that preprocesses intervals to collect readcounts and so on.
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