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

Somatic mutation detection in HLA regions using hg38 alt-aware alignments



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    David Benjamin

    Hi Elisabetta Manduchi, I'm not aware of anything to point you to for using alt contigs to call somatic variants in the HLA, but a good method along the lines of your first approach is the Polysolver pipeline developed by Sachet Shukla, our friend at MD Anderson Cancer Center.  

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    Elisabetta Manduchi

    Thank you David Benjamin. Indeed my first approach was along the lines of Polysolver. I've also tried to use the Polysolver docker itself as is, which however did not yield any results in my case.

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