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broadinstitute / gatk

Official code repository for GATK versions 4 and up
https://software.broadinstitute.org/gatk
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Genotyping only for a given genomic locus #7767

Open caixu0518 opened 2 years ago

caixu0518 commented 2 years ago

Hi GATK team,

I wonder if there are some parameters to only genotype a given genomic locus (many locos in bed format), i think this will accelerate the genotyping process instead of genotyping the whole genomic locus. Becuase sometimes, we only concerned about the genotypes of some known genomic locus.

my current command is '/src/gatk-4.1.3.0/gatk GenotypeGVCFs -R ChiifuIndex/Chiifu.fasta -V gendb://A01Genomicsdb -O A01_output.vcf.gz '

Best, Xu

rapaJiahe commented 2 years ago

Did you solve it? I also have the same problem.

droazen commented 2 years ago

@caixu0518 @rapaJiahe The -L argument in GATK lets you restrict the tool to a provided set of intervals. The intervals may be listed explicitly on the command line (eg., -L 1:1-100), or supplied in a file in one of the supported formats (.interval_list, .bed, etc.) -- eg., -L myintervals.bed)