#!/usr/bin/env python
from omics_pipe.parameters.default_parameters import default_parameters
from omics_pipe.utils import *
p = Bunch(default_parameters)
[docs]def call_variants(sample, call_variants_flag):
'''Calls variants from alignment .bam files using Varcall.
input:
Aligned.out.sort.bam or accepted_hits.bam
output:
.vcf file
citation:
Erik Aronesty (2011). ea-utils : "Command-line tools for processing biological sequencing data";
link:
https://code.google.com/p/ea-utils/wiki/Varcall
parameters from parameters file:
STAR_RESULTS:
GENOME:
VARSCAN_PATH:
VARSCAN_OPTIONS:
VARIANT_RESULTS:
TEMP_DIR:
SAMTOOLS_VERSION:
ANNOVAR_VERSION:
VCFTOOLS_VERSION:
VARSCAN_VERSION:
SAMTOOLS_OPTIONS:
'''
spawn_job(jobname = 'call_variants', 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 = "31gb", script = "/varcall_drmaa_bash.sh", args_list = [sample,p.STAR_RESULTS,p.GENOME, p.VARSCAN_PATH, p.VARSCAN_OPTIONS, p.VARIANT_RESULTS, p.TEMP_DIR, p.SAMTOOLS_VERSION, p.ANNOVAR_VERSION, p.VCFTOOLS_VERSION, p.VARSCAN_VERSION, p.SAMTOOLS_OPTIONS])
job_status(jobname = 'call_variants', resultspath = p.VARIANT_RESULTS, SAMPLE = sample, outputfilename = sample + "/variants.vcf", FLAG_PATH = p.FLAG_PATH)
return
if __name__ == '__main__':
call_variants(sample, call_variants_flag)
sys.exit(0)