Inputs Description

Input files and parameters required to run workflow

Common Parameters

Parameter

Description

Default

reference_fasta

Reference FASTA file

sample_name

The name of the sample submitted to the workflow

The entire workflow can be divided into 3 parts. 1. VARDICT workflow - consisting of calling the variants from VARDICT and normalizing and concatenating the complex and simple Variants in VCF format

Parameter

Description

Default

BedFile

Target file

Vardict_allele_frequency_threshold

Vardict

0.01

Minimum_allele_frequency

0.05

input_bam_case:

Input CH sample BAM file

Allele Depth

totalDepth

Total Depth

tnRatio

Tumor-Normal Variant Fraction ratio threshold

variantFraction

Tumor Variant fraction threshold

5.00E-05

minQual

Minimum variant call quality

allow_overlaps

First coordinate of the next file can precede last record of the current file

TRUE

stdout

Write to standard output, keep original files unchanged

TRUE

check-ref

what to do when incorrect or missing REF allele is encountered. 's' is to set/fix bad sites. Note that 's' can swap alleles and will update genotypes (GT) and AC counts, but will not attempt to fix PL or other fields. Also it will not fix strand issues in your VCF.

multiallelics

If multiallelic sites should be split or joined. '+'denotes that the biallelic sites should be joined into a multiallelic record.

output-type

Output type from BCFtools sort. 'z' denotes compressed VCF

preset

Input format for indexing

VCF

sample-name_vardict_STDFilter.txt

sample-name_single_filter_vcf

VCF file with filtered SNPs

sample-name_single_filer_complex.vcf

VCF file with filtered complex variant

sample-name_vardict_concatenated.vcf

VCF file with both complex and simple Variants

2. Variant Annotation - The VCF file from the before process is annotated with various files.

Parameter

Description

Default

retain_info

Comma-delimited names of INFO fields to retain as extra columns in MAF

CNT,TUMOR_TYPE

min_hom_vaf

If GT undefined in VCF, minimum allele fraction to call a variant homozygous

0.7

buffer_size

Number of variants VEP loads at a time; Reduce this for low memory systems

5000

custom_enst

List of custom ENST IDs that override canonical selection, in a file

input_cosmicCountDB_vcf

VCF file from COSMIC database with overall prevalence for a variant

input_cosmicprevalenceDB_vcf

VCF file from COSMIC database with lineage specific prevalence for a variant

input_complexity_bed

BED file with complex regions

input_mappability_bed

BED file with un-mappable regions

oncoKbApiToken

oncKB API token file

input_47kchpd_tsv_file

TSV file with 47k CH-PD variants

input_hotspot_tsv_file

TSV file with hotspots obtained from 47k CH-PD variants

input_panmeloid_tsv_file

TSV file with PAN-myeloid variants

opOncoKbMafName

output file name for MAF file that comes out of oncoKB annotation

output_complexity_filename

Output file name for MAF file annotated with complex regions

output_mappability_filename

Output file name for MAF file annotated with mappable regions

output_vcf2mafName

File name for VCF2MAF conversion

output_maf_name_panmyeloid

Output file name for MAF file annotated with PAN-myeloid dataset

output_47kchpd_maf_name

Output file name for MAF file annotated with 47k CH-PD variations

output_hotspot_maf_name

Output file name for MAF file annotated with hotspot variations

snpsift_countOpName

Output File name for VCF annotated with COSMIC prevalence

snpsift_prevalOpName

Output File name for VCF annotated with COSMIC lineage prevalence

column_name_complexity

Column name in the MAF file where complexity is annotated

column_name_mappability

Column name in the MAF file where mappability is annotated

output_column_name_panmyeloid

Column name in the MAF file where the presence of variants in PAN-Myeloid dataset is annotated

output_column_name_47kchpd

Column name in the MAF file where the presence of variants in 47k CH-PD dataset is annotated

output_column_name_hotspot

Column name in the MAF file where presence of variants in hotspot dataset is annotated

CH specific processing - where the MAF file from the above process is filtered and tagged, specifically for CH variants.

Parameter

Description

Default

output_maf_name_filer

Output MAF file name after filtering for CMO-CH criteria

output_maf_name_tag

Output MAF file name after tagging for CMO-CH criteria

Common workflow language execution engines accept two types of input that are JSON or YAML, please make sure to use one of these while generating the input file. For more information refer to: http://www.commonwl.org/user_guide/yaml/

Example Input YML file to run the CWL

reference_fasta: 
 class: File
 path: >-
    /juno/work/access/production/resources/reference/current/Homo_sapiens_assembly19.fasta
bedfile:
  class: File
  path: >-
    /work/bergerm1/bergerlab/charalk/projects/nucleo_qc/qc_generation_testing/CH_target_3bp.bed
input_bam_case: 
  class: File
  path: >-
    /path/to/bam/file.bam
input_cosmicCountDB_vcf: 
  class: File
  path: >-
    /work/cch/production/resources/cosmic/versions/v96/CosmicCodingMuts.vcf.gz
input_cosmicprevalenceDB_vcf: 
  class: File
  path: >-
    /work/cch/production/resources/cosmic/versions/v96/CosmicCodingMuts_GRCh37_processed.vcf.gz
input_complexity_bed: 
  class: File
  path:  >-
    /work/bergerm1/bergerlab/sivaprk/chipvar_resources/rmsk_mod.bed
input_mappability_bed: 
  class: File
  path:  >-
    /work/bergerm1/bergerlab/sivaprk/chipvar_resources/wgEncodeDacMapabilityConsensusExcludable_4cols.bed
oncoKbApiToken: 
  class: File
  path:  >-
    /work/bergerm1/bergerlab/sivaprk/chipvar_resources/apiToken.txt
input_47kchpd_tsv_file: 
  class: File
  path: >-
    /work/bergerm1/bergerlab/sivaprk/chipvar_resources/chpd47k_prevalence.tsv
input_hotspot_tsv_file: 
  class: File
  path: >-
    /work/bergerm1/bergerlab/sivaprk/chipvar_resources/hotspots_47kchpd.tsv
input_panmeloid_tsv_file: 
  class: File
  path: >-
    /work/bergerm1/bergerlab/sivaprk/chipvar_resources/pan_myeloid_ks.tsv 
opOncoKbMafName: sampleName_oncokb.maf
output_complexity_filename: sampleName_complexity.maf
output_mappability_filename: sampleName_mappability.maf
output_vcf2mafName: sampleName_vcf2maf.maf
concat_output_name: sampleName_concat.vcf.gz
retain_info:  CNT,TUMOR_TYPE
sample_name: sampleName
vardict_allele_frequency_threshold: 0
vardict_output_vcf_name: sampleName_vardict.vcf
snpsift_countOpName: sampleName_snpsift_cosmic.vcf
snpsift_prevalOpName: sampleName_snpsift_preval.vcf
column_name_complexity: complexity
column_name_mappability: mapability

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Last updated 8 months ago