How to get a SNPs file for chicken genome to be used for base-quality score recaliberation step of GATK variant calling
Dear All, I am quite new to the GATK tools. I would like to obtain a VCF file for known SNPs to be used in the base quality score recaliberation step of GATK. However, looking into the Ensemble, I have found only 'gallus_gallus.gvf.gz', which is not a VCF file as required by the GATK. I have also found variant VCF file on the European variation archive (https://www.ebi.ac.uk/eva/?Home) that I could export as a VCF file. Actually all papers is retrieving the known variant file from the dbSNPs. Also, there is no chicken genome available in GATK bunddle. Could anybody advice on how to best retrieve the VCF file needed in GATK ?
a) GATK version used: gatk4-220.127.116.11-0/gatk-package-18.104.22.168-local.jar version
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