Workflow: exome alignment and tumor-only variant detection

Fetched 2022-05-29 04:31:10 GMT
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Inputs

ID Type Title Doc
mills File
docm_vcf File
omni_vcf File
sequence https://w3id.org/cwl/view/git/336f7d1af649f42543baa6be2594cd872919b5b5/definitions/types/sequence_data.yml#sequence_data[]
trimming https://w3id.org/cwl/view/git/336f7d1af649f42543baa6be2594cd872919b5b5/definitions/types/trimming_options.yml#trimming_options (Optional)
vep_pick
dbsnp_vcf File
reference File
sample_name String
known_indels File
synonyms_file File (Optional)
vep_cache_dir Directory
bait_intervals File
bqsr_intervals String[] (Optional)
varscan_p_value Float (Optional)
target_intervals File target_intervals: interval_list file of targets used in the sequencing experiment

target_intervals is an interval_list corresponding to the targets for the capture reagent. Bed files with this information can be converted to interval_lists with Picard BedToIntervalList. In general for a WES exome reagent bait_intervals and target_intervals are the same.

summary_intervals https://w3id.org/cwl/view/git/336f7d1af649f42543baa6be2594cd872919b5b5/definitions/types/labelled_file.yml#labelled_file[]
varscan_min_reads Integer (Optional)
per_base_intervals https://w3id.org/cwl/view/git/336f7d1af649f42543baa6be2594cd872919b5b5/definitions/types/labelled_file.yml#labelled_file[]
vep_ensembl_species String

ensembl species - Must be present in the cache directory. Examples: homo_sapiens or mus_musculus

vep_ensembl_version String

ensembl version - Must be present in the cache directory. Example: 95

vep_to_table_fields String[] (Optional)
annotate_coding_only Boolean (Optional)
per_target_intervals https://w3id.org/cwl/view/git/336f7d1af649f42543baa6be2594cd872919b5b5/definitions/types/labelled_file.yml#labelled_file[]
varscan_min_coverage Integer (Optional)
varscan_min_var_freq Float (Optional)
vep_ensembl_assembly String

genome assembly to use in vep. Examples: GRCh38 or GRCm38

varscan_strand_filter Integer (Optional)
vep_custom_annotations https://w3id.org/cwl/view/git/336f7d1af649f42543baa6be2594cd872919b5b5/definitions/types/vep_custom_annotation.yml#vep_custom_annotation[]

custom type, check types directory for input format

qc_minimum_base_quality Integer (Optional)
target_interval_padding Integer target_interval_padding: number of bp flanking each target region in which to allow variant calls

The effective coverage of capture products generally extends out beyond the actual regions targeted. This parameter allows variants to be called in these wingspan regions, extending this many base pairs from each side of the target regions.

variants_to_table_fields String[] (Optional)
qc_minimum_mapping_quality Integer (Optional)
readcount_minimum_base_quality Integer (Optional)
picard_metric_accumulation_level String
readcount_minimum_mapping_quality Integer (Optional)
variants_to_table_genotype_fields String[] (Optional)
maximum_population_allele_frequency Float (Optional)

Steps

ID Runs Label Doc
index_cram
../tools/index_cram.cwl (CommandLineTool)
samtools index cram
bam_to_cram
../tools/bam_to_cram.cwl (CommandLineTool)
BAM to CRAM conversion
detect_variants Tumor-Only Detect Variants workflow
alignment_and_qc
alignment_exome.cwl (Workflow)
exome alignment with qc
pad_target_intervals
../tools/interval_list_expand.cwl (CommandLineTool)
expand interval list regions by a given number of basepairs

Outputs

ID Type Label Doc
cram File
final_tsv File
final_vcf File
flagstats File
hs_metrics File
varscan_vcf File
vep_summary File
annotated_vcf File
docm_gatk_vcf File
summary_hs_metrics File[]
insert_size_metrics File
per_base_hs_metrics File[]
verify_bam_id_depth File
insert_size_histogram File
per_target_hs_metrics File[]
verify_bam_id_metrics File
mark_duplicates_metrics File
alignment_summary_metrics File
per_base_coverage_metrics File[]
per_target_coverage_metrics File[]
tumor_snv_bam_readcount_tsv File
tumor_indel_bam_readcount_tsv File
Permalink: https://w3id.org/cwl/view/git/336f7d1af649f42543baa6be2594cd872919b5b5/definitions/pipelines/tumor_only_exome.cwl