author: Pawel Osipowski 8.3.2016

Script for calling and filtering small variants (SV) from short read data.

literature sources for pipeline: https://bcbio.wordpress.com/2014/05/12/wgs-trio-variant-evaluation http://bioinformatics.oxfordjournals.org/content/early/2014/07/03/bioinformatics.btu356

Pipeline:

1. Read correction and alignment: ./read_alignment.sh

2. Variant calling and filtering: ./variants_call.sh

3. Final max MD filtering of variants: ./maxmd_filter.sh

For details see shell scripts themselves