msk-access/chip-var

Workflow for calling and annotating CHIP variants

chip-var

This is a workflow for calling and annotating CHIP variants. The workflow calls the variants from the BAM file using vardict, which are then filtered based on the simple sample filtering criteria. The filtered variants are then processed, by sorting and normalizing and concating the complex and normal variants into a single VCF file. The concated variants are annotated with COSMIC prevalence counts and converted from VCF to MAF file format.

For detailed documentation refer to https://cmo-ci.gitbook.io/chip-variant-calling-and-processing/

Workflows used

• vardict workflow
• bcftools tabix
• bcftools norm
• bcftools sort
• snpift
• vcf2maf
• maf_annotated_by_bed
• maf_annotated_by_tsv
• maf_filter_cmoch
• maf_tag_cmoch

Usage

usage: chip-var.cwl [-h] --reference_fasta REFERENCE_FASTA --input_bam_case INPUT_BAM_CASE
                    [--bedfile BEDFILE] --sample_name SAMPLE_NAME
                    [--vardict_allele_frequency_threshold VARDICT_ALLELE_FREQUENCY_THRESHOLD]
                    [--retain_info RETAIN_INFO] --concat_output_name CONCAT_OUTPUT_NAME
                    [--vardict_output_vcf_name VARDICT_OUTPUT_VCF_NAME]
                    --input_cosmicprevalenceDB_vcf INPUT_COSMICPREVALENCEDB_VCF
                    --input_cosmicCountDB_vcf INPUT_COSMICCOUNTDB_VCF
                    [--snpsift_prevalOpName SNPSIFT_PREVALOPNAME]
                    [--snpsift_countOpName SNPSIFT_COUNTOPNAME] --input_complexity_bed
                    INPUT_COMPLEXITY_BED
                    [--output_complexity_filename OUTPUT_COMPLEXITY_FILENAME]
                    [--column_name_complexity COLUMN_NAME_COMPLEXITY] --oncoKbApiToken
                    ONCOKBAPITOKEN --opOncoKbMafName OPONCOKBMAFNAME
                    [--output_vcf2mafName OUTPUT_VCF2MAFNAME] --input_mappability_bed
                    INPUT_MAPPABILITY_BED
                    [--output_mappability_filename OUTPUT_MAPPABILITY_FILENAME]
                    [--column_name_mappability COLUMN_NAME_MAPPABILITY]
                    --input_47kchpd_tsv_file INPUT_47KCHPD_TSV_FILE --input_hotspot_tsv_file
                    INPUT_HOTSPOT_TSV_FILE --input_panmeloid_tsv_file INPUT_PANMELOID_TSV_FILE
                    [job_order]

chip-var

positional arguments:
  job_order             Job input json file

options:
  -h, --help            show this help message and exit
  --reference_fasta REFERENCE_FASTA
  --input_bam_case INPUT_BAM_CASE
  --bedfile BEDFILE
  --sample_name SAMPLE_NAME
  --vardict_allele_frequency_threshold VARDICT_ALLELE_FREQUENCY_THRESHOLD
  --retain_info RETAIN_INFO
  --concat_output_name CONCAT_OUTPUT_NAME
  --vardict_output_vcf_name VARDICT_OUTPUT_VCF_NAME
  --input_cosmicprevalenceDB_vcf INPUT_COSMICPREVALENCEDB_VCF
  --input_cosmicCountDB_vcf INPUT_COSMICCOUNTDB_VCF
  --snpsift_prevalOpName SNPSIFT_PREVALOPNAME
  --snpsift_countOpName SNPSIFT_COUNTOPNAME
  --input_complexity_bed INPUT_COMPLEXITY_BED
  --output_complexity_filename OUTPUT_COMPLEXITY_FILENAME
  --column_name_complexity COLUMN_NAME_COMPLEXITY
  --oncoKbApiToken ONCOKBAPITOKEN
  --opOncoKbMafName OPONCOKBMAFNAME
  --output_vcf2mafName OUTPUT_VCF2MAFNAME
  --input_mappability_bed INPUT_MAPPABILITY_BED
  --output_mappability_filename OUTPUT_MAPPABILITY_FILENAME
  --column_name_mappability COLUMN_NAME_MAPPABILITY
  --input_47kchpd_tsv_file INPUT_47KCHPD_TSV_FILE
  --input_hotspot_tsv_file INPUT_HOTSPOT_TSV_FILE
  --input_panmeloid_tsv_file INPUT_PANMELOID_TSV_FILE