mappability_snpable
This is a small bash script to run the snpable pipeline http://lh3lh3.users.sourceforge.net/snpable.shtml with minimal disk usage and parallelization.
usage:
bash snpable.bash [ref genome] [path to dir to seqbility]
seqbility is from lh3_misc from https://github.com/lh3/misc
example:
bash snpable.bash hg38.fa /storage/software/lh3_misc/seq/seqbility/
requires in path:
- bwa
- samtools
- gzip
- bgzip
- bedtools