[x] New feature (non-breaking change which adds functionality)
[x] Documentation update
How Has This Been Tested?
Please describe the tests that you ran to verify your changes. Provide instructions so we can reproduce. Please also list any relevant details for your test configuration
Description
This PR adds T1k to the BWA-GATK and Sentieon alignment workflows.
Change Log:
run_t1k
,hla_dna_ref_seqs
,hla_dna_gene_coords
,t1k_abnormal_unmap_flag
Part of https://d3b.atlassian.net/browse/BIXU-2332
Type of change
How Has This Been Tested?
Please describe the tests that you ran to verify your changes. Provide instructions so we can reproduce. Please also list any relevant details for your test configuration
Test Configuration:
Checklist: