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

(How to) Map reads to a reference with alternate contigs like GRCH38 Follow


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    Sonia Zumalave

    Very useful tutorial! However, it would be very useful if you specify how to get the reference alt index. Some of the links on the post are broken! thanks in advance. 

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    Andrew Skol

    Thank you for this summary of different ways of exploring the potential benefit of incorporating alternate loci into variant calling. I have two questions that I have been unable to find answers to elsewhere:

    1) Has a best practices workflow been established for variant calling when incorporating alternate loci, and

    2) It would seem that samples that have one haplotype derived from an alternative locus and one from the primary assembly present a challenge to variant calling, since as I understand it, any heterozygous position within this region would produce either 1) yield no variant if the alleles were the reference allele for their respective haplotypes or 2) a homozygous alt call for either the PA or ALT chromosome in the case where one of the alleles is non-reference for its chromosome, or 3) homozygous alt calls when both chromosomes possess non-reference alleles. Is there a way to "merge" these haplotype specific calls back to a diploid genotype?

    Thanks so much. 


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    Azza Ahmed


    Thank you for providing this tutorial. Would you kindly provide another link to the example data- perhaps on Google cloud or Terra? The ftp site is not working (I see it has been disabled as of June 2020:  Equally, the Google Drive link in the tutorial above ( is not working.


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