delangel ✭✭

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delangel
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Broad Institute
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  • Errors about input files having missing or incompatible contigs

    These errors occur when the names or sizes of contigs don't match between input files. This is a classic problem that typically happens when you get some files from collaborators, you try to use them… (View Post)
  • Can I use GATK on non-diploid organisms?

    (Image) In general most GATK tools don't care about ploidy. The major exception is, of course, at the variant calling step: the variant callers need to know what ploidy is assumed for a given sample … (View Post)
  • Using VariantEval

    This article has been deprecated in favor of a new method article which you can view here. For a complete, detailed argument reference, refer to the technical documentation page. Modules You can find… (View Post)
  • Which tools use pedigree information?

    There are two types of GATK tools that are able to use pedigree (family structure) information: Tools that require a pedigree to operate PhaseByTransmission and CalculateGenotypePosterior will not ru… (View Post)
  • Using Variant Annotator

    This document is out of date and has been retired. Please see the Annotation documentation in the Tool Docs as well as various other Guide articles for better materials on annotating variants. 2 SNPs… (View Post)