Place to store tools and scripts that make my work life easier
hla_vcf_liftover_merge.sh is a bash script to take the vcf files produced by SpecHLA (https://github.com/deepomicslab/SpecHLA) and converts them over to grch38 positions. It
used the files located in the HLA_liftover_refs folder, namely the chromosome 6 Human reference geneome fasta + dictionary files (bundles together as a tar.gz file) and the
liftover.chn file produced using flo (https://github.com/wurmlab/flo) a very fast ruby implementation of the UCSC liftover scripts. SpecHLA outputs a folder for each subject
in the out-directory. By listing all the subject directory names into a file sample_name.txt you can loop over every sample in your out-directory. Each gene vcf file is
lifted over to grch38 and then combined and sorted using bcftools. This final vcf file is then ready to be merged back into you main vcf file.