MSSNG DB6 Extract valid Chromosomes
Produce valid VCFs, one per chromosome. The vcf_samples_input is the GVCFtyper_file files from step 03 and the vcf_main input is either the GVCFtyper_main files also from step 03 or the GVCFtyper_main.recal recalibrated files from step 04 (depending on whether or not you want VQSR to be performed). region is a string containing the chromosome name only (e.g. chr1).all_samples is a TSV file with a single line with all sample names separated by
This is a companion discussion topic for the original entry at github.com/DNAstack/mssng-db6-exract-valid-chromosome-vcfs