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What is correct way to generate the input vcf and vcf.idx file for GATK4
We want to call SNVs by M2 for our WGS data. But, we do not have gnomad.vcf for WGS. So, we downloaded vcf files for each chr from gnomad website. Could you please let me know the "correct" way to generate both vcf and index file for GATK4 pipeline. Any suggestions are welcome! Thank you so much!
Does bcftools and tabix work?