--dbsnp option in HaplotypeCaller and other programsAnswered
GATK version 18.104.22.168
HaplotypeCaller and a couple of other programs (e.g. GenotypeGVCFs) have the option --dbsnp but I can not find any explanation what it does in the tool documentation. My guess is, that it annotates known variants with its variant ID in the ID field of the vcf file. So my question is: Is this assumption correct, and where is this documented?
Yes, the --dbsnp option will annotate the VCF with the dbsnp IDs for each sample. I was able to find a short explanation in the VariantAnnotator tool documentation.
Please let me know if you have any additional questions.
is a dbsnp file in HaplotypeCaller and a couple of other programs (e.g. GenotypeGVCFs) a file like dbsnp_146.hg38.vcf.gz, if germline mutation calling for Homo_sapiens?
Yes, that's correct! You can find some more information about the available resources and dbsnp files in the GATK Resource Bundle. Please let me know if you have any other questions.
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