def combine_variants(in_vcfs,
out_vcf,
in_reference_fasta=s['ref']['reference_fasta'],
genotype_merge_option='REQUIRE_UNIQUE',
mem_req=6 * 1024):
"""
:param genotype_merge_option: select from the following:
UNIQUIFY - Make all sample genotypes unique by file. Each sample shared across RODs gets named sample.ROD.
PRIORITIZE - Take genotypes in priority order (see the priority argument).
UNSORTED - Take the genotypes in any order.
REQUIRE_UNIQUE - Require that all samples/genotypes be unique.
"""
if genotype_merge_option == 'PRIORITIZE':
inputs = vcf_list_to_input([(i, p) for i, p in enumerate(in_vcfs)])
priority = '%s' % ','.join(map(str, range(len(in_vcfs))))
else:
inputs = vcf_list_to_input(in_vcfs)
priority = None
return r"""
{gatk} \
-T CombineVariants \
-R {in_reference_fasta} \
-o {out_vcf} \
{inputs} \
{args}
""".format(gatk=gatk(mem_req),
args=args(('-priority', priority),
('--genotypemergeoption', genotype_merge_option)),
**locals())
def combine_variants(in_vcfs,
out_vcf,
in_reference_fasta=s['ref']['reference_fasta'],
genotype_merge_option='REQUIRE_UNIQUE',
mem_req=6 * 1024):
"""
:param genotype_merge_option: select from the following:
UNIQUIFY - Make all sample genotypes unique by file. Each sample shared across RODs gets named sample.ROD.
PRIORITIZE - Take genotypes in priority order (see the priority argument).
UNSORTED - Take the genotypes in any order.
REQUIRE_UNIQUE - Require that all samples/genotypes be unique.
"""
if genotype_merge_option == 'PRIORITIZE':
inputs = vcf_list_to_input([(i, p) for i, p in enumerate(in_vcfs)])
priority = '%s' % ','.join(map(str, range(len(in_vcfs))))
else:
inputs = vcf_list_to_input(in_vcfs)
priority = None
return r"""
{gatk} \
-T CombineVariants \
-R {in_reference_fasta} \
-o {out_vcf} \
{inputs} \
{args}
""".format(gatk=gatk(mem_req),
args=args(('-priority', priority),
('--genotypemergeoption', genotype_merge_option)),
**locals())
def freebayes(reference_fasta=settings['ref']['reference_fasta'],
max_complex_gap=2,
no_complex=True,
in_target_bed=find('bed$'), in_bam=find('bam$'),
out_vcf=out_dir('variants.vcf')):
return r"""
{s[opt][freebayes]} -f {reference_fasta} \
--vcf {out_vcf} \
--targets {in_target_bed} \
{args} \
-m 30 -q 10 -R 0 -S 0 -F 0.1 \
{in_bam}
""".format(s=settings,
args=args(('--max-complex-gap', max_complex_gap),
('--no-complex', no_complex)),
**locals())
def freebayes(reference_fasta=settings['ref']['reference_fasta'],
max_complex_gap=2,
no_complex=True,
in_target_bed=find('bed$'),
in_bam=find('bam$'),
out_vcf=out_dir('variants.vcf')):
return r"""
{s[opt][freebayes]} -f {reference_fasta} \
--vcf {out_vcf} \
--targets {in_target_bed} \
{args} \
-m 30 -q 10 -R 0 -S 0 -F 0.1 \
{in_bam}
""".format(s=settings,
args=args(('--max-complex-gap', max_complex_gap),
('--no-complex', no_complex)),
**locals())
def cut_adapt(minimum_length=50,
in_fastq1=find('fq.gz|\.fastq|fastq.gz', tags=dict(read_pair='1')),
in_fastq2=find('fq.gz|\.fastq|fastq.gz', tags=dict(read_pair='2')),
out_fastq1=out_dir('trimmed_r1.fastq.gz'),
out_fastq2=out_dir('trimmed_r2.fastq.gz')):
# out_fastq1='>( gzip > %s)' % out_fastq1
# out_fastq2='>( gzip > %s)' % out_fastq2
return r"""
{s[opt][cutadapt]} \
-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC \
-A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT \
{args} \
-o {out_fastq1} -p {out_fastq2} \
{in_fastq1} {in_fastq2}
""".format(s=s,
args=args(('--minimum-length', minimum_length)),
**locals())
def cut_adapt(minimum_length=50,
in_fastq1=find('fq.gz|\.fastq|fastq.gz',
tags=dict(read_pair='1')),
in_fastq2=find('fq.gz|\.fastq|fastq.gz',
tags=dict(read_pair='2')),
out_fastq1=out_dir('trimmed_r1.fastq.gz'),
out_fastq2=out_dir('trimmed_r2.fastq.gz')):
# out_fastq1='>( gzip > %s)' % out_fastq1
# out_fastq2='>( gzip > %s)' % out_fastq2
return r"""
{s[opt][cutadapt]} \
-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC \
-A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT \
{args} \
-o {out_fastq1} -p {out_fastq2} \
{in_fastq1} {in_fastq2}
""".format(s=s,
args=args(('--minimum-length', minimum_length)),
**locals())