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Helper scripts for bcbio-nextgen

Requirements: Git, Conda

To install:

git clone [email protected]:bcbio/bcbio-utils.git
conda env create --name bcbio-utils --file bcbio-utils/environment.yml

If you would like to use CWL scripts you will need to install cwltool separately:

conda activate bcbio-utils
pip install cwltool

Scripts:

  • analyze_complexity_by_starts.py - create reads sequenced vs unique start sites graph for examining the quality of a library
  • analyze_quality_recal.py - provide plots summarizing recalibration of quality scores
  • bam_to_fastq_region.py - prepare paired end fastq files from a chromosome region in an aligned input BAM file
  • bam_to_wiggle.py - convert BAM files to BigWig file format in a specified region
  • bcbio_prep_cwl_genomes.py - clean and prepare a set of genomes for CWL usage and upload
  • broad_redo_analysis.py - redo post-processing of Broad alignments with updated pipeline
  • build_compare_vcf.py - build a test comparison dataset from an existing VCF file
  • build_gatk_jar.sh - build a GATK jar without embedded dependencies from current git
  • cg_svevents_to_vcf.py - convert Complete Genomics SvEvents file of structural variants to VCF
  • collect_metrics_to_csv.py - collect alignment summary metrics from multiple lanes and summarize as CSV
  • convert_samplesheet_config.py - convert Illumina SampleSheet CSV files to the run_info.yaml input file
  • find_clonal_svs.py - find 10x structural variants present uniquely in parent or clones
  • format_dream_truthset.py - format DREAM challenge truth sets to contain BED files of covered regions and SVs
  • gb2genome.py - convert genbank to gtf
  • hla_loh_comparison.py - run LOH heterogeneity comparison amongst multiple methods, focusing on HLA
  • hlas_to_pgroups.py - collapse HLAs present in hg38 1000 genomes distribution to p-groups
  • hydra_to_vcf.py - convert Hydra BEDPE output into VCF 4.1 format
  • monthly_billing_report.py - retrieve from Galaxy a high level summary report of sequencing done in a month
  • plink_to_vcf.py - convert Plink ped/map files into VCF format using plink and Plink/SEQ
  • rename_samples.py - rename sample name in a BAM file, eliminating spaces and colon characters
  • resort_bam_karyotype.py - resort a BAM file karyotypically to match GATK's preferred file order
  • rtg_to_callable.py - convert RTG coverage statistics into a BED file of callable regions
  • sort_gatk_intervals.py - sort GATK interval lists based on a sequence dictionary
  • summarize_gemini_tstv.py - provide table summarizing Transition/Transversion ratios for variants
  • summarize_priority_variants.py - summarize priority calls in annotated structural variants
  • summarize_timing.py - convert time stamps from bcbio logs into hourly timings per step
  • tcga_to_bcbio.py - handle pairing primary and metastasized tumors with blood or solid normals
  • test_resources.py - ?
  • upload_to_synapse.py - upload bcbio reference materials and inputs to a Synapse project