def normalize_vap_leftalign(orig_vcf, conf):
orig_vcf = util.sort_vcf(orig_vcf, conf)
tmp_vcf = orig_vcf.replace(".vcf", ".vap.tmp.vcf").replace(".gz", "")
final_vcf = orig_vcf.replace(".vcf", ".vap.leftaligned.vcf")
norm_orig_cmd = conf.get('main', 'vcfallelicprimitives') + " " + orig_vcf
subprocess.check_call(norm_orig_cmd, shell=True, stdout=file(tmp_vcf, 'w'))
no_et = ""
try:
no_et = " -et NO_ET -K " + conf.get('main', 'gatk_no_et')
except:
pass
cmd = "java -Djava.io.tmpdir=. -Xmx1g -jar " + conf.get('main', 'gatk') + " -T LeftAlignAndTrimVariants " + no_et + " -R " + conf.get('main', 'ref_genome') + " -U ALLOW_SEQ_DICT_INCOMPATIBILITY -V " + tmp_vcf + " -o " + final_vcf
subprocess.check_call(cmd, shell=True)
return util.bgz_tabix(final_vcf, conf)
def normalize_vap_leftalign(orig_vcf, conf):
err = open("/dev/null")
orig_vcf = util.sort_vcf(orig_vcf, conf)
tmp_vcf = orig_vcf.replace(".vcf", ".vap.tmp.vcf").replace(".gz", "")
final_vcf = orig_vcf.replace(".vcf", ".vap.leftaligned.vcf")
norm_orig_cmd = conf.get('main', 'vcfallelicprimitives_path') + " " + orig_vcf
tmp_output=subprocess.check_output(norm_orig_cmd, shell=True)
with open(tmp_vcf, "w") as fh:
fh.write(tmp_output)
no_et = ""
try:
no_et = " -et NO_ET -K " + conf.get('main', 'gatk_no_et')
except:
pass
cmd = "java -Djava.io.tmpdir=. -Xmx1g -jar " + conf.get('main', 'gatk_path') + " -T LeftAlignAndTrimVariants " + no_et + " -R " + conf.get('main', 'ref_genome') + " -V " + tmp_vcf + " -o " + final_vcf
subprocess.check_output(cmd, shell=True)
err.close()
return util.bgz_tabix(final_vcf, conf)
def call_variant_fb(bam, orig_genome_path, bed, conf=None):
vcfoutput = "output-fb.vcf"
cmd = [conf.get("main", "freebayes_path"), "-f", orig_genome_path, "-t", bed, "-b", bam, "-v", vcfoutput]
subprocess.check_output(cmd)
return util.sort_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)
