コード例 #1
0
def _piped_realign_gatk(data, region, cl, out_base_file, tmp_dir, prep_params):
    """Perform realignment with GATK, using input commandline.
    GATK requires writing to disk and indexing before realignment.
    """
    broad_runner = broad.runner_from_config(data["config"])
    pa_bam = "%s-prealign%s" % os.path.splitext(out_base_file)
    if not utils.file_exists(pa_bam):
        with file_transaction(data, pa_bam) as tx_out_file:
            cmd = "{cl} -o {tx_out_file}".format(**locals())
            do.run(cmd, "GATK re-alignment {0}".format(region), data)
    bam.index(pa_bam, data["config"])
    recal_file = realign.gatk_realigner_targets(
        broad_runner,
        pa_bam,
        data["sam_ref"],
        data["config"],
        region=region_to_gatk(region),
        known_vrns=dd.get_variation_resources(data))
    recal_cl = realign.gatk_indel_realignment_cl(
        broad_runner,
        pa_bam,
        data["sam_ref"],
        recal_file,
        tmp_dir,
        region=region_to_gatk(region),
        known_vrns=dd.get_variation_resources(data))
    return pa_bam, recal_cl
コード例 #2
0
def _piped_realign_gatk(data, region, cl, out_base_file, tmp_dir):
    """Perform realignment with GATK, using input commandline.
    GATK requires writing to disk and indexing before realignment.
    """
    broad_runner = broad.runner_from_config(data["config"])
    pa_bam = "%s-prealign%s" % os.path.splitext(out_base_file)
    if not utils.file_exists(pa_bam):
        with file_transaction(pa_bam) as tx_out_file:
            subprocess.check_call("{cl} > {tx_out_file}".format(**locals()),
                                  shell=True)
    broad_runner.run_fn("picard_index", pa_bam)
    dbsnp_vcf = shared.configured_ref_file("dbsnp", data["config"],
                                           data["sam_ref"])
    recal_file = realign.gatk_realigner_targets(broad_runner,
                                                pa_bam,
                                                data["sam_ref"],
                                                dbsnp=dbsnp_vcf,
                                                region=region_to_gatk(region))
    recal_cl = realign.gatk_indel_realignment_cl(broad_runner,
                                                 pa_bam,
                                                 data["sam_ref"],
                                                 recal_file,
                                                 tmp_dir,
                                                 region=region_to_gatk(region))
    return pa_bam, " ".join(recal_cl)
コード例 #3
0
ファイル: bamprep.py プロジェクト: senthil10/bcbio-nextgen
def _piped_realign_gatk(data, region, cl, out_base_file, tmp_dir, prep_params):
    """Perform realignment with GATK, using input commandline.
    GATK requires writing to disk and indexing before realignment.
    """
    broad_runner = broad.runner_from_config(data["config"])
    pa_bam = "%s-prealign%s" % os.path.splitext(out_base_file)
    if not utils.file_exists(pa_bam):
        with file_transaction(pa_bam) as tx_out_file:
            pipe = ">" if prep_params["dup"] else "-o"
            cmd = "{cl} {pipe} {tx_out_file}".format(**locals())
            do.run(cmd, "GATK pre-alignment {0}".format(region), data)
    bam.index(pa_bam, data["config"])
    dbsnp_vcf = data["genome_resources"]["variation"]["dbsnp"]
    recal_file = realign.gatk_realigner_targets(broad_runner,
                                                pa_bam,
                                                data["sam_ref"],
                                                dbsnp=dbsnp_vcf,
                                                region=region_to_gatk(region))
    recal_cl = realign.gatk_indel_realignment_cl(broad_runner,
                                                 pa_bam,
                                                 data["sam_ref"],
                                                 recal_file,
                                                 tmp_dir,
                                                 region=region_to_gatk(region))
    return pa_bam, " ".join(recal_cl)
コード例 #4
0
ファイル: bamprep.py プロジェクト: nickholz/bcbio-nextgen
def _piped_realign_gatk(data, region, cl, out_base_file, tmp_dir, prep_params):
    """Perform realignment with GATK, using input commandline.
    GATK requires writing to disk and indexing before realignment.
    """
    broad_runner = broad.runner_from_config(data["config"])
    pa_bam = "%s-prealign%s" % os.path.splitext(out_base_file)
    if not utils.file_exists(pa_bam):
        with file_transaction(data, pa_bam) as tx_out_file:
            cmd = "{cl} -o {tx_out_file}".format(**locals())
            do.run(cmd, "GATK pre-alignment {0}".format(region), data)
    bam.index(pa_bam, data["config"])
    recal_file = realign.gatk_realigner_targets(
        broad_runner,
        pa_bam,
        data["sam_ref"],
        data["config"],
        region=region_to_gatk(region),
        known_vrns=dd.get_variation_resources(data),
    )
    recal_cl = realign.gatk_indel_realignment_cl(
        broad_runner,
        pa_bam,
        data["sam_ref"],
        recal_file,
        tmp_dir,
        region=region_to_gatk(region),
        known_vrns=dd.get_variation_resources(data),
    )
    return pa_bam, " ".join(recal_cl)
コード例 #5
0
ファイル: bamprep.py プロジェクト: luwening/bcbio-nextgen
def _piped_realign_gatk(data, region, cl, out_base_file, tmp_dir):
    """Perform realignment with GATK, using input commandline.
    GATK requires writing to disk and indexing before realignment.
    """
    broad_runner = broad.runner_from_config(data["config"])
    pa_bam = "%s-prealign%s" % os.path.splitext(out_base_file)
    if not utils.file_exists(pa_bam):
        with file_transaction(pa_bam) as tx_out_file:
            subprocess.check_call("{cl} > {tx_out_file}".format(**locals()), shell=True)
    broad_runner.run_fn("picard_index", pa_bam)
    recal_file = realign.gatk_realigner_targets(broad_runner, pa_bam, data["sam_ref"],
                      dbsnp=shared.configured_ref_file("dbsnp", data["config"], data["sam_ref"]),
                      region=_region_to_gatk(region))
    recal_cl = realign.gatk_indel_realignment_cl(broad_runner, pa_bam, data["sam_ref"],
                                                 recal_file, tmp_dir, region=_region_to_gatk(region))
    return pa_bam, " ".join(recal_cl)
コード例 #6
0
ファイル: bamprep.py プロジェクト: brentp/bcbio-nextgen
def _piped_realign_gatk(data, region, cl, out_base_file, tmp_dir, prep_params):
    """Perform realignment with GATK, using input commandline.
    GATK requires writing to disk and indexing before realignment.
    """
    broad_runner = broad.runner_from_config(data["config"])
    pa_bam = "%s-prealign%s" % os.path.splitext(out_base_file)
    if not utils.file_exists(pa_bam):
        with file_transaction(pa_bam) as tx_out_file:
            pipe = ">" if prep_params["dup"] else "-o"
            cmd = "{cl} {pipe} {tx_out_file}".format(**locals())
            do.run(cmd, "GATK pre-alignment {0}".format(region), data)
    broad_runner.run_fn("picard_index", pa_bam)
    dbsnp_vcf = data["genome_resources"]["variation"]["dbsnp"]
    recal_file = realign.gatk_realigner_targets(broad_runner, pa_bam, data["sam_ref"],
                                                dbsnp=dbsnp_vcf, region=region_to_gatk(region))
    recal_cl = realign.gatk_indel_realignment_cl(broad_runner, pa_bam, data["sam_ref"],
                                                 recal_file, tmp_dir, region=region_to_gatk(region))
    return pa_bam, " ".join(recal_cl)