#!/usr/bin/env python
from omics_pipe.parameters.default_parameters import default_parameters
from omics_pipe.utils import *
p = Bunch(default_parameters)
[docs]def filter_variants(sample, filter_variants_flag):
'''Filters variants to remove common variants.
input:
.bam or .sam file
output:
.vcf file
citation:
Piskol et al. 2013. Reliable identification of genomic variants from RNA-seq data. The American Journal of Human Genetics 93: 641-651.
link:
http://lilab.stanford.edu/SNPiR/
parameters from parameters file:
VARIANT_RESULTS:
TEMP_DIR:
SAMTOOLS_VERSION:
BWA_VERSION:
PICARD_VERSION:
GATK_VERSION:
BEDTOOLS_VERSION:
UCSC_TOOLS_VERSION:
GENOME:
REPEAT_MASKER:
SNPIR_ANNOTATION:
RNA_EDIT:
DBSNP:
MILLS:
G1000:
WORKING_DIR:
BWA_RESULTS:
SNPIR_VERSION:
SNPIR_CONFIG:
SNPIR_DIR:
SNPEFF_VERSION:
dbNSFP:
VCFTOOLS_VERSION:
WORKING_DIR:
SNP_FILTER_OUT_REF:
'''
spawn_job(jobname = 'filter_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 = "28gb", script = "/filter_snpir_drmaa.sh", args_list = [p.VARIANT_RESULTS, p.TEMP_DIR, p.SAMTOOLS_VERSION, p.BWA_VERSION, p.PICARD_VERSION, p.GATK_VERSION, p.BEDTOOLS_VERSION, p.UCSC_TOOLS_VERSION, p.GENOME, p.REPEAT_MASKER, p.SNPIR_ANNOTATION, p.RNA_EDIT, p.DBSNP, p.MILLS, p.G1000, p.WORKING_DIR, sample, p.BWA_RESULTS, p.SNPIR_VERSION, p.SNPIR_CONFIG, p.SNPIR_DIR, p.SNPEFF_VERSION, p.dbNSFP, p.VCFTOOLS_VERSION, p.WORKING_DIR, p.SNP_FILTER_OUT_REF])
job_status(jobname = 'filter_variants', resultspath = p.VARIANT_RESULTS, SAMPLE = sample, outputfilename = sample + "/intogen_input.vcf", FLAG_PATH = p.FLAG_PATH)
return
if __name__ == '__main__':
filter_variants(sample, filter_variants_flag)
sys.exit(0)