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- Samir Amin
Hi Sheila, I wonder if gatk 18.104.22.168 Mutect2 includes a patch related to following reply from a developer, i.e., including germline hets AF for tumor-only somatic calling. Also, if I set up af-of-alleles-not-in-resource = 0, wouldn't it render use …
This is not related to primary discussion but thought it's important for gistic2 input format. In my earlier post, I mentioned to convert log2(copy_number_raw_value) - 1. However, that should not be applicable to GATK or most other copy number cal…
Thanks for this excellent documentation. About gistic2, it is something that took a while for us to get it running for dog genome. Here are some tips. GISTIC2 takes segment copy number value as log2(raw value) - 1, so as to convert resulting CN valu…
XT is bwa specific tag1,2 XT tag, e.g. XT:A:U = unique mapper; XT:A:R = more than 1 high-scoring matches FN is probably number of read features in each record3.
Great and many thanks! This pretty much resolves my current issue.
Hi @sutturka , I have been referred by @shlee from following discussion. I am working on canine glioma genome. For somatic variant calling using GATK4 workflow and specifically creating PON and Filtering calls, I wonder if we can talk over getting …
hi @shlee, That was very helpful and so as this document in running M2. Thanks! I have now merged WGS and exome bam files for tumor and normal. While merging, I kept RGSM in identical for each of merged tumor and normal, e.g., merged_sample1_tumor…
Hi everyone, I like to revisit this question and see if there is any change in suggestion over last five years. In my case, I am working on canine genome WGS and WES tumor/normal pairs. I have them aligned using GATK3 best practices. Given we have …