REQUIRED for all errors and issues:
a) GATK version used: docker image: tutorial_11682_11683:gatk18.104.22.168
b) Exact command used:
gatk --java-options "-Xmx3g" CollectAllelicCounts \
-I sample.bam \ -R reference.fa \ -L sites.interval_list \ -O sample.allelicCounts.tsv
I was able to reproduce the results following tutorials 11682 and 11683. However, when I use my own data, I am unsure where and how I can obtain the required input `sites.interval_list`. The region that I am interested is the whole genome, what should I use as the input of this interval list?
If possible, could you also direct me to the resources I can use to understand the copy ratio plots results of somatic CNV? The germline CNV workflow resulted in some VCF, which makes me wonder if there are variants specific results produced by somatic CNV workflow.
Thank you very much!
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