def GATKpreprocessing(infile, outfile):
'''Reorders BAM according to reference fasta and add read groups using
SAMtools, realigns around indels and recalibrates base quality scores
using GATK'''
to_cluster = USECLUSTER
track = P.snip(os.path.basename(infile), ".bam")
tmpdir_gatk = P.getTempDir()
job_memory = PARAMS["gatk_memory"]
genome = "%s/%s.fa" % (PARAMS["bwa_index_dir"], PARAMS["genome"])
outfile1 = outfile.replace(".bqsr", ".readgroups.bqsr")
outfile2 = outfile.replace(".bqsr", ".realign.bqsr")
PipelineExome.GATKReadGroups(infile, outfile1, genome,
PARAMS["readgroup_library"],
PARAMS["readgroup_platform"],
PARAMS["readgroup_platform_unit"])
PipelineExome.GATKIndelRealign(outfile1, outfile2, genome,
PARAMS["gatk_threads"])
IOTools.zapFile(outfile1)
PipelineExome.GATKBaseRecal(outfile2, outfile, genome,
PARAMS["gatk_dbsnp"],
PARAMS["gatk_solid_options"])
IOTools.zapFile(outfile2)
def realignMatchedSample(infile, outfile):
''' repeat realignments with merged bam of control and tumor
this should help avoid problems with sample-specific realignments'''
genome = "%s/%s.fa" % (PARAMS["bwa_index_dir"], PARAMS["genome"])
PipelineExome.GATKIndelRealign(infile, outfile, genome)
IOTools.zapFile(infile)