elcortegano
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Latest activity by elcortegano-
elcortegano commented,
I'm getting this error on GATK4-4.2.1.0-0. It only seems to appear enabling `--mitochondria-mode true`, but I need this option.
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elcortegano commented,
Hi Pamela, The need for QUAL and MQ at invariant sites mainly comes from "backward" compatibility with a 2015 Genome Research study (https://pubmed.ncbi.nlm.nih.gov/26260971/). There, de novo mutat...
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elcortegano commented,
Hi Pamela, thank you for your feedback, The problem with `GenotypeGVCFs -all-sites` is that in gatk v.4.x (and v.3.x) is that I do not get QUAL or MQ for any invariant site (wonder if might be due ...
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elcortegano commented,
Ok, I found a tarball here: https://github.com/broadgsa/gatk-protected/releases/tag/2.8 I guess I want to reformulate my question as how to find the jar file of this version, pre-compiled. It is pr...
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elcortegano created a post,
Where do I find GATK v2.8-1?
Hi all, This might perhaps an XY problem, since my real problem with GATK is the need to compute QUAL and MQ values for invariant sites, which does not seem to be possible with versions 3.x and 4.x...