Build Pacific cod reference SNP panel from WGS data

[laurahspencer]

I would like help building a reference SNP panel for pacific cod using the big heatwave genetics dataset (see issue #2232). Panel should be a VCF containing genotypes at biallelic SNPs, and should be phased (if possible?). If there are samples with unusually low coverage please don’t include them. The goal will be to use this for genotype imputation in other low coverage datasets, so I would err on high quality thresholds for filtering. I believe GATK is the best program to use for this.

[laurahspencer]

This is in process