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

No depth information in INFO column

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    David Benjamin

    Jay Singh Your command generates a GVCF.  If you are doing joint calling, you must merge the single-sample GVCFs with GenotypeGVCFs.  If you are doing single-sample calling you should remove -ERC GVCF from your command.

    I'm guessing that the DP INFO field is missing from the "reference block" GVCF lines where the only alt allele is <NON-REF>, but present in all others.  If so, everything will be fine after GenotypeGVCFs.

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    Jay Singh

    Dear David

    Thanks for the reply.

    Yes You are right. DP INFO field is missing from the "reference block" GVCF lines where the only alt allele is <NON-REF>, but present in all others.

    Thanks.

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