
elcortegano
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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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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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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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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...