#!/usr/bin/env python
from omics_pipe.parameters.default_parameters import default_parameters
from omics_pipe.utils import *
p = Bunch(default_parameters)
[docs]def GATK_preprocessing_WGS(sample, GATK_preprocessing_WGS_flag):
'''GATK preprocessing steps for whole genome sequencing.
input:
sorted.rg.md.bam
output:
.ready.bam
citation:
McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA (2010). The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20:1297-303.
link:
http://www.broadinstitute.org/gatk/
parameters from parameters file:
BWA_RESULTS:
TEMP_DIR:
GATK_VERSION:
GENOME:
DBSNP:
MILLS:
G1000:
SAMTOOLS_VERSION:
'''
spawn_job(jobname = 'GATK_preprocessing_WGS', SAMPLE = sample, LOG_PATH = p.LOG_PATH, RESULTS_EMAIL = p.RESULTS_EMAIL, SCHEDULER = p.SCHEDULER, walltime = "240:00:00", queue = p.QUEUE, nodes = "1", ppn = "8", memory = "15gb", script = "/GATK_preprocessing_WGS_" + p.GATK_VERSION + ".sh", args_list = [p.BWA_RESULTS, sample, p.TEMP_DIR,p.GATK_VERSION, p.GENOME, p.DBSNP,p.MILLS,p.G1000, p.SAMTOOLS_VERSION])
job_status(jobname = 'GATK_preprocessing_WGS', resultspath = p.BWA_RESULTS, SAMPLE = sample, outputfilename = sample + "/" + sample + ".ready.bam", FLAG_PATH = p.FLAG_PATH)
return
if __name__ == '__main__':
GATK_preprocessing_WGS(sample, GATK_preprocessing_WGS_flag)
sys.exit(0)