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example_input.yml
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example_input.yml
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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
output_maf_name_panmyeloid: sampleName_panmyeloid.maf
output_47kchpd_maf_name: sampleName_47kchpd.maf
output_hotspot_maf_name: sampleName_hotspot.maf
output_maf_name_filer: sampleName_filtered.maf
output_maf_name_tag: sampleName_tagged.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
output_column_name_panmyeloid: panmyeloid
output_column_name_47kchpd: 47kchpd
output_column_name_hotspot: hotspot