Designed to run on a vm pulling from an object store therefore may need to change src_cmd variables to point to correct novarc file. Files also have expected suffixes

Wrapper script to run an edited version of metalfox (original was obtained here: https://github.com/cpwardell/bin/blob/master/metalfox.py) to calculate foxoG scored for each variant

./metalfox_pipe.py -j <config_file> -sp <sample_pairs_list> -r <reference_mount> 

Input description:

config_file: json-formatted text file. See example file - only relevant variables are: 'tools':'metalfox', 'refs':'cont', 'refs':'obj', 'refs':'mapability', 'params':'threads', 'params':'ram'

sample_pairs_list: tumor normal pairs as bionimbus ids, formatted as such: 2016-123_2016-124 2016-123 2016-124

reference_mount: Cinder block mount point or directory in which references have been downloaded in ephemeral mount

Can be run separately from above wrapper if only one sample to be used. Need to have downloaded relevant files ahead of time

./metalfox.py -f1 full path to exome directory -f full path to MuTect call_stats.out file -f3 full path to bam
-m mapability file

Input description:

f1: Not sure and haven't used it. It's optional and we haven't needed it for our purposes.

f: The .out file from mutect calls

f3: bam file that used for the .out output

m: optional mapability file

Runs picard CollectOxoGMetrics which give a sample/bam file global damage scores for each base change type. Scores above 30 are considered little to no damage, 20-30, concerning, and below 20 severe.

./oxog_check.py  -j <config_file> -f <lane_list> -r <reference_mount>

Input description:

config_file: json-formatted text file. See example file - only relevant variables are: 'tools':'java', 'tools':'picard', 'refs':'fa_ordered','refs':'intervals', 'refs':'cont', 'refs':'obj', 'params':'threads', 'params':'ram'

lane_list: Individual sample lane list in format:

2016-129 capture 160308_D00422_0286_BHKH5JBCXX_1, 160308_D00422_0286_BHKH5JBCXX_2

2016-128 capture 160308_D00422_0286_BHKH5JBCXX_1, 160308_D00422_0286_BHKH5JBCXX_2

reference_mount: Cinder block mount point or directory in which references have been downloaded in ephemeral mount

Downloads reports and adjusts based out metalfox output showing only variants that passed, limited to on-target

./calc_score_output_pass.py <pair_list> <config_file>

Input description:

pair_list: tumor normal pairs as bionimbus ids, formatted as such:

2016-123_2016-124 2016-123 2016-124

config_file: json-formatted text file. See example file - only relevant variables are: 'refs':'cont', 'refs':'annotation'

Summarizes all samples oxog damage from output of oxog_check.py

./oxog_summary.py <file_list> <suffix>

Input description:

file_list: List of files output from oxog_check

suffix: File suffix from output to remove from headers. Typically '.oxo_summary.txt'