This directory contains various scripts used by the pipeline.
A python script that retrieves unbiased ASE counts of reads overlapping STRs using WASP-corrected counts of reads from SNPs nearby.
A python script for lifting over TSVs whose first two columns are CHROM and POS, respectively.
A python script to create plots of allele specific expression vs STR repeat number. It also fits simple linear regression models to the plots.
A python script for sorting STRs by a custom importance metric consisting of the number of supporting samples, the distance from the nearest SNP, and the strength of the ASE at the nearest SNP.
A python script that can be used to remove variants with empty ALT records in a VCF.
A python script that can be used to unphase the genotypes in a VCF in preparation for use by BEAGLE. This script is used by the prepare pipeline.