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

Issues with LiftoverVcf GRch37 to GRch38

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    Eric Nguyen

    If I switch to a hg19 to hg38 chain file (adding "chr" to the chromosome numbers) I get 80% of variants fail to liftover instead of 100%. 

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    Gökalp Çelik

    Hi Eric Nguyen

    Can you share the sequence dictionary of the original vcf file and also can you try this tool using the latest version available?

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    VivekTodur

    My source vcf and target genome do not have alt sequences, but the chain file downloaded from UCSC has it and is causing the issue...

    Any solution to this problem? 

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    Gökalp Çelik

    Hi VivekTodur

    liftover chain files are crafted specific for source and target genomes therefore modifications to those files are not recommended. If you wish to create your own liftover chains you may check UCSC's documentation on liftover from the link below.

    https://genomewiki.ucsc.edu/index.php/LiftOver_Howto 

    On the other hand if you are dealing with only primary contigs for liftover, you may temporarily move your variants to a genome with alt contigs, remove liftovers that hit alt contigs and replace sequence dictionary with the one you are interested therefore you will have most of your variants lifted over without issues. However you need to pay attention compatibility of reference contigs across both target genomes. Unless they are compatible then you may face non-matching reference nucleotide issues in downstream applications.

    I hope this helps. 

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