GenotypeGVCF - missed SNP ID

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Salma H. Elaksher

• January 26, 2024 12:08

REQUIRED for all errors and issues:
a) GATK version used: GATK 4.4.0
b) Exact command used:
java -Xmx8G gatk-package-4.4.0.0-local.jar GenotypeGVCFs -R "$Ref" -V $chr.gvcf.gz -O GVCFall.vcf

i missed SNP ID column(III) after applying GenotypeGVCFs, is there any way to solve this

c) Entire program log:
 

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  Louis Bergelson

  • February 12, 2024 21:14

  Hi Salma H. Elaksher,

  I think you're saying that your output vcf is missing rsID tags for known variants? 

  If you want those added to your file when doing GenotypeGvcfs, you have to include the --dbsnp argument, and a dbSnp vcf with the tags you want to use.  Otherwise it will not be populated.  

  Since you've already genotyped these, you can annotate the existing vcf by running it through VariantAnnotator with the --dbsnp argument.

  I hope that helps. 

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