dv-trio takes in a trio (father-mother-child) of bam files and calls variants using DeepVariant and a post-processing pipeline to eliminate mendelian errors.
Clone this repository into your cloud instance and run the install_dependencies.sh script. This will install all dependencies onto your instance's PATH.
Usage:
$(basename $0) -f father -m mother -c child -s sex -r reference [ -o output ] [ -t threshold ] [ -b bucket ]
Post-processes trio calls made by DeepVariant to correct for Mendelian errors.
Required arguments:
-f <father> path to bam file of father sample
-m <mother> path to bam file of mother sample
-c <child> path to bam file of child sample
-s <sex> sex of child (m/f)
-r <reference> path to reference file
Options:
-o <output> path to desired output directory (defaults to current directory)
-t <threshold> likelihood ratio cutoff threshold (float b/w 0 and 1, default is 0.3)
-b <bucket> S3 bucket path to write output to
-h this help message