Comments (1)
I figured it out. The normalization step had not yet been run for this vcf. After running the normalization step and getting rid of duplicates, the combine step worked fine.
bcftools norm -Oz -o scalpel.hg38.sites.norm.vcf.bgz -f /restricted/projectnb/casa/ref/GRCh38_full_analysis_set_plus_decoy_hla.fa -d all -cs scalpel.hg38.sites.vcf.gz
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from bayestyper.