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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

GenotypeGVCF Output Only 1 Locus

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    danilovkiri

    Hi Himawari

    CombineGVCFs for combining GVCFs is perfectly fine.

    If you have checked the order of GVCF, then I advise you to check again. Look at the first VCF entry for chromosome 1 (contig 1) and the last. Have a glimpse at all the positions in your GVCF for chromosome 1.

    Additionally, look at the GVCF header (bcftools view -O v -h ) and grep it for entries starting with `##contig=<ID=`. You might find an erroneous entry for chromosome 1. 

    If not found, run GATK ValidateVariants (https://gatk.broadinstitute.org/hc/en-us/articles/360037057272-ValidateVariants) specifying --validate-GVCF and --reference <reference_genome.fa> file (used for genotyping).It might give a hint on what is wrong with your GVCF. If anything strange found, please, post here the full header of the GVCF, the first 10 entries of your VCF (not header), warnings and full error logs.

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