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

Liftover Picard hg19 to hg38: variants were not successfully lifted over



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    Andres Caballero

    In case someone finds this post, I finally managed to solve it by using a different chain file downloaded from Ensembl (GRCh37_to_GRCh38.chain.gz). The one I was using (downloaded from UCSC) was the one causing the issue. 

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    Hassan Alikhani

    Same problem here. Considering your note on using the GRCh37_to_GRCh38.chain.gz chain file, I found that the issue is related to chromosome names. If chromosome names in your VCF are like 1, 2, X, M, etc., you can't use the hg19ToHg38.over.chain.gz chain file. There are two solutions:

    1. Change chromosome names in the VCF using bcftools annotate --rename-chrs.
    2. Use GRCh37_to_GRCh38.chain.gz instead of hg19ToHg38.over.chain.gz.
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