def run_haplotype_caller(args):
blue("Going for STAGE_6 - run_haplotype_caller")
with cwd(joiner(args.hg, "chromFa")):
cmd = (
"module add "
+ ngs_tools_dict["GATK"]
+ " && $GATK_RUN -T HaplotypeCaller -R hg19.fa -I recal_reads.bam -L chr20 --genotyping_mode DISCOVERY -stand_call_conf 30 -stand_emit_conf 10 -o raw_variants.vcf"
)
run_command(cmd, Exception)
ok("Done!")
def marking_PCR_duplicates(args):
blue("Going for STAGE_3 - marking_PCR_duplicates")
with cwd(joiner(args.hg, "chromFa")):
cmd = (
"module add "
+ ngs_tools_dict["Picard"]
+ " && $PICARDRUN MarkDuplicates INPUT=output.bam OUTPUT=output.marked.bam METRICS_FILE=metrics CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT"
)
run_command(cmd, Exception)
ok("done")
def SAM_to_BAM_conversion(args):
blue("Going for STAGE_2 - SAM_to_BAM_conversion")
with cwd(joiner(args.hg, "chromFa")):
cmd = (
"module add "
+ ngs_tools_dict["Picard"]
+ " && $PICARDRUN SortSam SO=coordinate INPUT=out.sam OUTPUT=output.bam VALIDATION_STRINGENCY=LENIENT CREATE_INDEX=true"
)
run_command(cmd, Exception)
ok("done")
def actual_alignment(args):
blue("Going for STAGE_1 - actual_alignment")
with cwd(joiner(args.hg, "chromFa")):
cmds = [
"module add " + ngs_tools_dict["bwa"] + " && bwa aln -t 4 -f input.sai hg19 input.fastq",
"module add "
+ ngs_tools_dict["bwa"]
+ ' && bwa samse -f out.sam -r "@RG\tID:bwa\tLB:Exome1Lib\tSM:Exome1Sampl\tPL:ILLUMINA" hg19 input.sai input.fastq',
]
run_commands(cmds, Exception)
ok("done")
def quality_score_recalibration(args):
blue("Going for STAGE_5 - quality_score_recalibration")
with cwd(joiner(args.hg, "chromFa")):
cmds = [
"module add "
+ ngs_tools_dict["GATK"]
+ " && $GATK_RUN -T BaseRecalibrator -R hg19.fa -I input_bam.marked.realigned.fixed.bam -L chr20 -knownSites dbsnp_138.hg19.vcf -o recal_data.table",
"module add "
+ ngs_tools_dict["GATK"]
+ " && $GATK_RUN -T PrintReads -R hg19.fa -I input_bam.marked.realigned.fixed.bam -L chr20 -BQSR recal_data.table -o recal_reads.bam",
]
run_commands(cmds, Exception)
ok("Done!")
def local_realignment(args):
blue("Going for STAGE_4 - local_realignment")
with cwd(joiner(args.hg, "chromFa")):
cmds = [
"module add "
+ ngs_tools_dict["GATK"]
+ " && $GATK_RUN -T RealignerTargetCreator -R hg19.fa -o input.bam.list -I output.marked.bam",
"module add "
+ ngs_tools_dict["GATK"]
+ " && $GATK_RUN -I output.marked.bam -R hg19.fa -T IndelRealigner -targetIntervals input.bam.list -o input.marked.realigned.bam",
"module add "
+ ngs_tools_dict["Picard"]
+ " && $PICARDRUN FixMateInformation INPUT=input.marked.realigned.bam OUTPUT=input_bam.marked.realigned.fixed.bam SO=coordinate VALIDATION_STRINGENCY=LENIENT CREATE_INDEX=true",
]
run_commands(cmds, Exception)
ok("Done!")