def call_variant_gatk_hc(bam, orig_genome_path, bed, conf=None):
vcfoutput = "output-hc.vcf"
err = open("/dev/null")
no_et = ""
try:
no_et = " -et NO_ET -K " + conf.get("main", "gatk_no_et")
except:
pass
cmd = (
"java -Xmx1g -Djava.io.tmpdir=. -jar "
+ conf.get("main", "gatk_path")
+ " -T HaplotypeCaller "
+ no_et
+ " -R "
+ orig_genome_path
+ " -I "
+ bam
+ " -L "
+ bed
+ " -o "
+ vcfoutput
)
subprocess.check_output(cmd, shell=True, stderr=err)
err.close()
return util.compress_vcf(vcfoutput, conf)
def call_variant_gatk_hc(bam, genome, bed, conf=None):
vcfoutput = "output-hc.vcf"
cmd='''java -Xmx1g -Djava.io.tmpdir=. -jar {gatk} -T HaplotypeCaller -R {genome} -I {bam} -U ALLOW_SEQ_DICT_INCOMPATIBILITY \
-L {bed} -o {vcfoutput}'''
cmd = cmd.format(gatk=conf.get('main', 'gatk'), genome=genome, bam=bam, bed=bed, vcfoutput=vcfoutput)
subprocess.check_call(cmd, stdout=open('/dev/null'), stderr=subprocess.STDOUT, shell=True)
return util.compress_vcf(vcfoutput, conf)
def call_variant_gatk_hc_emit_all(bam, genome, bed, conf=None):
vcfoutput = "output-hc.vcf"
no_et = ""
try:
no_et = " -et NO_ET -K " + conf.get('main', 'gatk_no_et')
except:
pass
cmd="java -Xmx1g -Djava.io.tmpdir=. -jar " + conf.get('main', 'gatk') + " -T HaplotypeCaller -stand_emit_conf 1.0 " + no_et + " -R " + genome +" -I " + bam + " -U ALLOW_SEQ_DICT_INCOMPATIBILITY -L " + bed + " -o " + vcfoutput
subprocess.check_call(cmd, stdout=open('/dev/null'), stderr=subprocess.STDOUT)
return util.compress_vcf(vcfoutput, conf)
def call_variant_gatk_ug(bam, genome, bed, conf=None):
vcfoutput = "output-ug.vcf"
no_et = ""
try:
no_et = " -et NO_ET -K " + conf.get('main', 'gatk_no_et')
except:
pass
cmd="java -Xmx1g -Djava.io.tmpdir=. -jar " + conf.get('main', 'gatk') + " -T UnifiedGenotyper -glm BOTH " + no_et + " -R " + genome +" -I " + bam + " -L " + bed + " -o " + vcfoutput
subprocess.check_call(cmd, stdout=open('/dev/null'), stderr=subprocess.STDOUT)
return util.compress_vcf(vcfoutput, conf)
def call_wecall(bam, orig_genome_path, bed, conf=None):
vcfoutput = "output-wc.vcf"
cmd = (
conf.get("main", "wecall_path")
+ " --refFile "
+ orig_genome_path
+ " --inputs "
+ bam
+ " --regions "
+ bed
+ " --output "
+ vcfoutput
)
subprocess.check_call(cmd, shell=True)
return util.compress_vcf(vcfoutput, conf)
def call_variant_platypus(bam, orig_genome_path, bed, conf=None):
vcfoutput = "output-platypus.vcf"
cmd = (
"python "
+ conf.get("main", "platypus_path")
+ " callVariants --refFile "
+ orig_genome_path
+ " --bamFiles "
+ bam
+ " --regions "
+ bed
+ " -o "
+ vcfoutput
)
subprocess.check_call(cmd, shell=True)
return util.compress_vcf(vcfoutput, conf)
def call_variant_fb_minrepeatentropy(bam, orig_genome_path, bed, conf=None):
vcfoutput = "output-fb.vcf"
cmd = [
conf.get("main", "freebayes_path"),
"-f",
orig_genome_path,
"--min-repeat-entropy",
"1",
"-t",
bed,
"-b",
bam,
"-v",
vcfoutput,
]
subprocess.check_output(cmd)
return util.compress_vcf(vcfoutput, conf)
def call_variant_sentieon_hc(bam, genome, bed, conf=None):
vcfoutput = "output-sentieonhc.vcf"
cmd='{sentieon} driver -r {genome} -i {bam} --algo Haplotyper {vcfoutput}'
cmd=cmd.format(sentieon=conf.get('main', 'sentieon'), genome=genome, bam=bam, vcfoutput=vcfoutput)
subprocess.check_call(cmd, stdout=open('/dev/null'), stderr=subprocess.STDOUT, shell=True)
return util.compress_vcf(vcfoutput, conf)
def call_wecall(bam, genome, bed, conf=None):
vcfoutput = "output-wc.vcf"
cmd=conf.get('main', 'wecall') + " --refFile " + genome + " --inputs " + bam + " --regions " + bed + " --output " + vcfoutput
subprocess.check_call(cmd, stdout=open('/dev/null'))
return util.compress_vcf(vcfoutput, conf)
def call_variant_platypus(bam, genome, bed, conf=None):
vcfoutput = "output-platypus.vcf"
cmd= "python " + conf.get('main', 'platypus') + " callVariants --refFile " + genome + " --bamFiles " + bam + " --regions " + bed + " -o " + vcfoutput
subprocess.check_call(cmd, stdout=open('/dev/null'))
return util.compress_vcf(vcfoutput, conf)
def call_variant_fb_minrepeatentropy(bam, genome, bed, conf=None):
vcfoutput = "output-fb.vcf"
cmd=[conf.get('main', 'freebayes'), "-f", genome, "--no-partial-observations", "--min-repeat-entropy", "1", "-t", bed, "-b", bam, "-v", vcfoutput]
subprocess.check_call(cmd, stdout=open('/dev/null'))
sorted_vcf = util.sort_vcf(vcfoutput, conf)
return util.compress_vcf(sorted_vcf, conf)
def call_variant_fb(bam, genome, bed, conf=None):
vcfoutput = "output-fb.vcf"
cmd=[conf.get('main', 'freebayes'), "-f", genome, "-t", bed, "-b", bam, "-v", vcfoutput]
subprocess.check_call(cmd, stdout=open('/dev/null'))
sorted_vcf = util.sort_vcf(vcfoutput, conf)
return util.compress_vcf(sorted_vcf, conf)
def call_variant_platypus_asm(bam, genome, bed, conf=None):
vcfoutput = "output-platypus.vcf"
cmd= "python " + conf.get('main', 'platypus') + " callVariants --assemble=1 --assembleBadReads=1 --refFile " + genome + " --bamFiles " + bam + " --regions " + bed + " -o " + vcfoutput
subprocess.check_call(cmd)
return util.compress_vcf(vcfoutput, conf)
