def command(self): return "zcat" + \ required(" ", self.input) + \ "| vcffilter " + \ required("-f ", self.filter) + \ "| bgzip " + required(" > ", self.output) + \ " && tabix -p vcf {output}".format(output=self.output)
def command(self): required("", self.input_reference_sequence_fai) return "curl -L " + \ required(" ", self.remote) + \ "| gzip -d |" + vt_split_and_leftaln(self.input_reference_sequence, allow_ref_mismatches=True) + \ "| bgzip " + required(" > ", self.output) + \ " && tabix -p vcf {output}".format(output=self.output)
def command(self): cmd = "cp " + \ required(" ", self.input) + \ required(" ", self.output) if self.input.endswith(".bam"): cmd += " && samtools index {}".format(self.output) return cmd
def command(self): return "picard -XX:ParallelGCThreads=1 MergeSamFiles " + \ repeat("INPUT=", self.input_bams) + \ required("ASSUME_SORTED=", str(self.assume_sorted).lower()) + \ required("MERGE_SEQUENCE_DICTIONARIES=", str(self.merge_dicts).lower()) + \ required("OUTPUT=", self.output_bam) + \ " && samtools index " + required("", self.output_bam)
def command(self): return "picard -XX:ParallelGCThreads=1 -Xmx5g CollectGcBiasMetrics CHART=/dev/null" + \ required("I=", self.input) + \ required("O=", self.output_metrics) + \ required("S=", self.output_summary) + \ required("R=", self.reference_sequence) + \ optional("STOP_AFTER=", self.stop_after)
def command(self): return "picard -XX:ParallelGCThreads=1 CollectWgsMetrics " + \ required("I=", self.input) + \ required("R=", self.reference_sequence) + \ required("O=", self.output_metrics) + \ optional("MINIMUM_MAPPING_QUALITY=", self.minimum_mapping_quality) + \ optional("MINIMUM_BASE_QUALITY=", self.minimum_base_quality) + \ optional("COVERAGE_CAP=", self.coverage_cap)
def command(self): return "cat " + \ required(" ", self.input) + \ " | bgzip " + \ required(" > ", self.output) + \ " && tabix " + \ optional("-p ", self.filetype) + \ " {} ".format(self.output)
def command(self): qdnaseq2bed_cmd = "qdnaseq2bed.py -n segments " + \ required("-i ", self.input_segments) + \ "| sort -k1,1 -k2,2n " + \ "| bedtools median -c 5 -o mean " + \ required("-a ", self.genes_gtf) + " -b - " + \ "| cnvgtf2bed.py -i /dev/stdin -n gene_id " + \ required("> ", self.output_bed) return qdnaseq2bed_cmd
def command(self): return "picard -Xmx5g -XX:ParallelGCThreads=1 " + \ required("-Djava.io.tmpdir=", self.scratch) + \ " MarkDuplicates " + \ required("INPUT=", self.input_bam) + \ required("METRICS_FILE=", self.output_metrics) + \ required("OUTPUT=", self.output_bam) + \ conditional(self.remove_duplicates, "REMOVE_DUPLICATES=true") + \ " && samtools index " + required("", self.output_bam)
def command(self): return "picard -XX:ParallelGCThreads=1 CollectHsMetrics " + \ required("I=", self.input) + \ required("R=", self.reference_sequence) + \ required("O=", self.output_metrics) + \ required("TI=", self.target_regions) + \ required("BI=", self.bait_regions) + \ optional("BAIT_SET_NAME=", self.bait_name) + \ repeat('METRIC_ACCUMULATION_LEVEL=', self.accumulation_level)
def command(self): haplotypecaller_cmd = "gatk {} HaplotypeCaller ".format(self.java_options) + \ required(" -R ", self.reference_sequence) + \ required(" -I ", self.input_bam) + \ " -L " + self.interval_list + \ " --dbsnp " + self.dbSNP + \ required(" -O ", self.output) return haplotypecaller_cmd
def command(self): # compileMetadata 3098121 3098849 --db_config $HOME/repos/reportgen/tests/referral-db-config.json \ # --output /dev/stdout --address_table_file reportgen/assets/addresses.csv return "compileMetadata" + \ required('', self.blood_barcode) + \ required('', self.tumor_barcode) + \ required('--db_config ', self.referral_db_conf) + \ required('--address_table_file ', self.addresses) + \ required('--output ', self.output_json)
def command(self): return "gatk-klevebring -T HeterozygoteConcordance " + \ required("-R ", self.reference_sequence) + \ required("-V ", self.input_vcf) + \ required("-I ", self.input_bam) + \ required("-sid ", self.normalid) + \ optional("-L ", self.target_regions) + \ conditional(self.filter_reads_with_N_cigar, "--filter_reads_with_N_cigar") + \ required("-o ", self.output)
def command(self): tag_cmd = "" if self.tag: tag_cmd = "echo \"# {}\" >> {} \n".format(self.tag, self.output) return "echo \"# bedtools-coverage-hist: {}\"".format(self.input_bam) + \ required("d>", self.output) + "\n" + \ tag_cmd + \ "bedtools coverage -hist " + \ required("-a ", self.input_bed) + \ required("-b ", self.input_bam) + \ "|grep \"^all\" " + required(">> ", self.output)
def command(self): required("", self.input_tumor) required("", self.input_normal) freq_filter = ( " bcftools filter -e 'STATUS !~ \".*Somatic\"' 2> /dev/null " "| %s -c 'from autoseq.util.bcbio import depth_freq_filter_input_stream; import sys; print depth_freq_filter_input_stream(sys.stdin, %s, \"%s\")' " % (sys.executable, 0, 'bwa')) somatic_filter = ( " sed 's/\\.*Somatic\\\"/Somatic/' " # changes \".*Somatic\" to Somatic "| sed 's/REJECT,Description=\".*\">/REJECT,Description=\"Not Somatic via VarDict\">/' " "| %s -c 'from autoseq.util.bcbio import call_somatic; import sys; print call_somatic(sys.stdin.read())' " % sys.executable) blacklist_filter = " | intersectBed -a . -b {} | ".format( self.blacklist_bed) cmd = "vardict-java " + required("-G ", self.reference_sequence) + \ optional("-f ", self.min_alt_frac) + \ required("-N ", self.tumorid) + \ optional("-r ", self.min_num_reads) + \ " -b \"{}|{}\" ".format(self.input_tumor, self.input_normal) + \ " -c 1 -S 2 -E 3 -g 4 -Q 10 " + required("", self.target_bed) + \ " | testsomatic.R " + \ " | var2vcf_paired.pl -P 0.9 -m 4.25 -M " + required("-f ", self.min_alt_frac) + \ " -N \"{}|{}\" ".format(self.tumorid, self.normalid) + \ " | " + freq_filter + " | " + somatic_filter + " | " + fix_ambiguous_cl() + " | " + remove_dup_cl() + \ " | vcfstreamsort -w 1000 " + \ " | " + vt_split_and_leftaln(self.reference_sequence) + \ " | bcftools view --apply-filters .,PASS " + \ " | vcfsorter.pl {} /dev/stdin ".format(self.reference_dict) + \ conditional(blacklist_filter, self.blacklist_bed) + \ " | bgzip > {output} && tabix -p vcf {output}".format(output=self.output) return cmd
def command(self): required("", self.input_tumor) required("", self.input_normal) tmp_vcf = "{scratch}/{uuid}.vcf.gz".format(scratch=self.scratch, uuid=uuid.uuid4()) # run vardict without removing non-somatic variants, and adding "SOMATIC" INFO field for somatic variants vardict_cmd = "vardict-java " + required("-G ", self.reference_sequence) + \ optional("-f ", self.min_alt_frac) + \ required("-N ", self.tumorid) + \ optional("-r ", self.min_num_reads) + \ " -b \"{}|{}\" ".format(self.input_tumor, self.input_normal) + \ " -c 1 -S 2 -E 3 -g 4 -Q 10 " + required("", self.target_bed) + \ " | testsomatic.R " + \ " | var2vcf_paired.pl -P 0.9 -m 4.25 " + required("-f ", self.min_alt_frac) + \ " -N \"{}|{}\" ".format(self.tumorid, self.normalid) + \ " | " + fix_ambiguous_cl() + " | " + remove_dup_cl() + \ " | sed 's/Somatic;/Somatic;SOMATIC;/g' " + \ " | sed '/^#CHROM/i ##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Somatic event\">' " + \ " | vcfstreamsort -w 1000 " + \ " | bcftools view --apply-filters .,PASS " + \ " | vcfsorter.pl {} /dev/stdin ".format(self.reference_dict) + \ " | bgzip > " + tmp_vcf + " && tabix -p vcf " + tmp_vcf # annotate variants with dbSNP id annotate_cmd = "bcftools annotate --annotation {} --columns ID ".format(self.dbsnp) + \ " --output-type z --output {} ".format(self.output) + tmp_vcf + \ " && tabix -p vcf {}".format(self.output) # remove temporary vcf and tabix rm_tmp_cmd = "rm " + tmp_vcf + "*" return " && ".join([vardict_cmd, annotate_cmd, rm_tmp_cmd])
def command(self): activate_env_cmd = "source activate qdnaseqenv" qdnaseq_cmd = "qdnaseq.R " + \ required("--bam ", self.input) + \ required("--output ", self.output) + \ optional("--background ", self.background) deactivate_env_cmd = "source deactivate" return "{} && {} && {} ".format( activate_env_cmd, qdnaseq_cmd, deactivate_env_cmd, )
def command(self): regions_file = "{scratch}/{uuid}.regions".format(scratch=self.scratch, uuid=uuid.uuid4()) bed_to_regions_cmd = "cat {} | bed_to_regions.py > {}".format( self.target_bed, regions_file) call_somatic_cmd = " | {} -c 'from autoseq.util.bcbio import call_somatic; import sys; print call_somatic(sys.stdin.read())' ".format( sys.executable) freebayes_cmd = "freebayes-parallel {} {} ".format(regions_file, self.threads) + \ required("-f ", self.reference_sequence) + " --use-mapping-quality " + \ optional("--min-alternate-fraction ", self.min_alt_frac) + \ optional("--min-coverage ", self.min_coverage) + \ conditional(self.use_harmonic_indel_quals, "--harmonic-indel-quality") + \ optional("", self.params) + \ repeat(" ", self.input_bams) + \ """| bcftools filter -i 'ALT="<*>" || QUAL > 5' """ + \ "| filter_erroneus_alt.py -V /dev/stdin " + \ conditional(self.somatic_only, call_somatic_cmd) + \ " | " + vt_split_and_leftaln(self.reference_sequence) + \ " | vcfuniq | bcftools view --apply-filters .,PASS " + \ " | bgzip > {output} && tabix -p vcf {output}".format(output=self.output) # reason for 'vcfuniq': freebayes sometimes report duplicate variants that need to be uniqified. rm_regions_cmd = "rm {}".format(regions_file) return " && ".join([bed_to_regions_cmd, freebayes_cmd, rm_regions_cmd])
def command(self): tmpdir = "{}/write-alascca-report-{}".format(self.scratch, uuid.uuid4()) mkdir_tmp_cmd = "mkdir -p {}".format(tmpdir) tmp_pdf = os.path.join(tmpdir, 'Report.pdf') cmd = 'writeAlasccaReport ' + \ required(' --tmp_dir ', tmpdir) + \ required(' --output_dir ', tmpdir) + \ conditional(self.alascca_only, " --alascca_only ") + \ required('', self.input_genomic_json) + \ required('', self.input_metadata_json) cp_cmd = "cp {} {}".format(tmp_pdf, self.output_pdf) rmdir_cmd = "rm -r {}".format(tmpdir) return " && ".join([mkdir_tmp_cmd, cmd, cp_cmd, rmdir_cmd])
def command(self): output_prefix = "{scratch}/msisensor-{uuid}".format( scratch=self.scratch, uuid=uuid.uuid4()) output_table = "{}".format(output_prefix) output_dis = "{}_dis".format(output_prefix) output_germline = "{}_germline".format(output_prefix) output_somatic = "{}_somatic".format(output_prefix) return "msisensor msi " + \ required("-d ", self.msi_sites) + \ required("-n ", self.input_normal_bam) + \ required("-t ", self.input_tumor_bam) + \ required("-o ", output_prefix) + \ required("-b ", self.threads) + \ " && cp {} {}".format(output_prefix, self.output) + \ " && rm {} {} {} {}".format(output_table, output_dis, output_germline, output_somatic)
def command(self): required("", self.input_bam) required("", self.reference_sequence) # configuration configure_strelkagermline = "configureStrelkaGermlineWorkflow.py " + \ " --bam " + self.input_bam + \ " --ref " + self.reference_sequence + \ " --targeted --callRegions " + self.target_bed + \ " --runDir " + self.output_dir cmd = configure_strelkagermline + " && " + self.output_dir + "/runWorkflow.py -m local -j 20" filter_passed_variants = "zcat " + self.output_dir + "/results/variants/variants.vcf.gz" + \ " | awk 'BEGIN { OFS = \"\\t\"} /^#/ { print $0 } {if($7==\"PASS\") print $0 }' " + \ " | bgzip > {output} && tabix -p vcf {output}".format(output=self.output_filtered_vcf) return " && ".join([cmd, filter_passed_variants])
def command(self): fork = "" if self.threads > 1: # vep does not accept "--fork 1", so need to check. fork = " --fork {} ".format(self.threads) cmdstr = "vep --vcf --output_file STDOUT " + \ self.additional_options + required("--dir ", self.vep_dir) + \ required("--fasta ", self.reference_sequence) + \ required("-i ", self.input_vcf) + \ " --check_existing --total_length --allele_number " + \ " --no_escape --no_stats --everything --offline " + \ " --custom {},,vcf,exact,0,ClinicalSignificance ".format(self.brca_exchange_vcf) + \ fork + " > " + required("", self.output_vcf) # " && tabix -p vcf {}".format(self.output_vcf) return cmdstr
def command(self): return "alasccaCNA.R " + \ required("--cnr ", self.input_cnr) + \ required("--cns ", self.input_cns) + \ required("--germlinevcf ", self.input_germline_vcf) + \ required("--somaticvcf ", self.input_somatic_vcf) + \ required("--chrsizes ", self.chrsizes) + \ required("--png ", self.output_png) + \ required("--json.cna ", self.output_cna) + \ required("--json.purity ", self.output_purity)
def command(self): return 'compileAlasccaGenomicReport ' + \ required('', self.input_somatic_vcf) + \ required('', self.input_cn_calls) + \ required('', self.input_msisensor) + \ required('--tumorCovJSON ', self.input_tcov_qc) + \ required('--normalCovJSON ', self.input_ncov_qc) + \ required('--purityJSON ', self.input_purity_qc) + \ required('--contaminationJSON ', self.input_contam_qc) + \ required('--output ', self.output_json)
def command(self): bgzip = "" fork = "" if self.threads > 1: # vep does not accept "--fork 1", so need to check. fork = " --fork {} ".format(self.threads) if self.output_vcf.endswith('gz'): bgzip = " | bgzip " cmdstr = "variant_effect_predictor.pl --vcf --output_file STDOUT " + \ self.additional_options + required("--dir ", self.vep_dir) + \ required("--fasta ", self.reference_sequence) + \ required("-i ", self.input_vcf) + \ " --check_alleles --check_existing --total_length --allele_number " + \ " --no_escape --no_stats --everything --offline " + \ fork + bgzip + " > " + required("", self.output_vcf) + \ " && tabix -p vcf {}".format(self.output_vcf) return cmdstr
def command(self): if not self.reference and not self.targets_bed: raise ValueError("Either reference or targets_bed must be supplied") if self.reference and self.targets_bed: raise ValueError("Supply either reference OR targets_bed") tmpdir = "{}/cnvkit-{}".format(self.scratch, uuid.uuid4()) sample_prefix = stripsuffix(os.path.basename(self.input_bam), ".bam") cnvkit_cmd = "cnvkit.py batch " + required("", self.input_bam) + \ optional("-r ", self.reference) + \ conditional(self.targets_bed, "--fasta " + str(self.fasta) + " --split ") + \ conditional(self.targets_bed, "-n") + \ optional("-t ", self.targets_bed) + \ required("-d ", tmpdir) copy_cns_cmd = "cp {}/{}.cns ".format(tmpdir, sample_prefix) + required(" ", self.output_cns) copy_cnr_cmd = "cp {}/{}.cnr ".format(tmpdir, sample_prefix) + required(" ", self.output_cnr) rm_cmd = "rm -r {}".format(tmpdir) return " && ".join([cnvkit_cmd, copy_cns_cmd, copy_cnr_cmd, rm_cmd])
def command(self): filt_vcf = "{scratch}/{uuid}.vcf.gz".format(scratch=self.scratch, uuid=uuid.uuid4()) bgzip = "" tabix = "" if self.output.endswith('gz'): bgzip = "| bgzip" tabix = " && tabix -p vcf {}".format(self.output) filt_vcf_cmd = "vcf_filter.py --no-filtered " + required("", self.input_vcf) + " sq --site-quality 5 " + \ "|bgzip" + " > " + filt_vcf vcf_add_sample_cmd = "vcf_add_sample.py " + \ conditional(self.filter_hom, "--filter_hom") + \ required("--samplename ", self.samplename) + \ filt_vcf + " " + \ required("", self.input_bam) + \ bgzip + " > " + self.output + tabix rm_filt_cmd = "rm " + filt_vcf return " && ".join([filt_vcf_cmd, vcf_add_sample_cmd, rm_filt_cmd])
def command(self): # activating conda env activate_cmd = "source activate purecn-env" # running PureCN running_cmd = "PureCN.R " + required("--out ", self.outdir) + \ required("--sampleid ", self.tumorid) + \ required("--segfile ", self.input_seg) + \ required("--tumor ", self.input_cnr) + \ required("--vcf ", self.input_vcf) + \ required("--genome ", self.genome) + \ optional("--funsegmentation ", self.funseg) + \ optional("--minpurity ", self.minpurity) + \ optional("--hzdev ", self.hzdev) + \ optional("--maxnonclonal ", self.maxnonclonal) + \ optional("--minaf ", self.minaf) + \ optional("--error ", self.error) + \ conditional(self.postopt, "--postoptimize") # deactivating the conda env deactivate_cmd = "conda deactivate" # touching required output files touch_cmd = "touch {} {} {} {}".format(self.out_csv, self.out_genes, self.out_variants, self.output) return " && ".join( [activate_cmd, running_cmd, deactivate_cmd, touch_cmd])
def command(self): required("input_files", self.input_files) required("output_base", self.output) required("dir_to_search", self.search_dir) basefn = os.path.basename(self.output) odir = os.path.dirname(self.output) return "multiqc " + \ required("", self.search_dir) + \ required("-o ", odir) + \ optional("-n ", basefn) + \ optional("-k ", self.data_format) + \ optional("-i ", self.report_title) + \ " --data-dir --zip-data-dir -v -f"
def command(self): return "extract_coverage_caveat.py " + \ required(" ", self.input_histogram) + \ required("--high-thresh-fraction ", self.high_thresh_fraction) + \ required("--high-thresh-fold-cov ", self.high_thresh_fold_cov) + \ required("--low-thresh-fraction ", self.low_thresh_fraction) + \ required("--low-thresh-fold-cov ", self.low_thresh_fold_cov) + \ required("> ", self.output)