Added a reference downloader to both versions.
You need to have hs37d5.fa, hs37d5.fa.fai, hg19.fa and hg19.fa.fai in reference subdirectory.
hs37d5.fa.gz + fai can be downloaded from:
https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/
hg19.fa.gz + fai can be downloaded from:
https://omic.tech/ftp/public/3dsnp/assembly/
Notice! You have to decompress and index with samtools faidx both of the above references!
Simple instructions:
Copy all of the bams you want to include in source directory and run the program. The result will be in target subdirectory.
The Bash version works also on Windows using MSYS2 shell.