Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

HaplotypeCaller Follow

2 comments

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    Jonathan Klonowski

    What purpose does --pedigree serve?

    It says "Pedigree file for determining the population "founders"", but I do not understand what the output is or what that output can be used for.

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    Joshua Burdick

    I think that there may be a typo in the "Single-sample GVCF calling with allele-specific annotations" section. It suggests the options "-G Standard -G AS_Standard". However, when using those, I get an error: "Unrecognized annotation group name: Standard" .

    After looking through the GATK4 workflow at:
    https://github.com/gatk-workflows/gatk4-germline-snps-indels/blob/master/haplotypecaller-gvcf-gatk4.wdl
    I changed those options to "-G StandardAnnotation -G AS_StandardAnnotation", which didn't throw that error. (I don't know whether it is working, though, as I'm new to using GATK.)

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