Workflow: Downsample and HaplotypeCaller

Fetched 2023-01-05 07:10:16 GMT
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Inputs

ID Type Title Doc
ploidy Integer (Optional)
intervals 1fb5d593cc0a0a1fd66ff270199af66c[]

arrays of intervals to use in each individual run of the haplotypecaller

reference File

The reference that was used for the already-completed alignments

read_filter String (Optional)
downsample_seed Integer (Optional)
variant_index_type
crams_to_downsample https://w3id.org/cwl/view/git/06d2440d115b446c299b4ce96e8812d2f8df86ec/definitions/pipelines/downsample_and_recall.cwl#crams_to_downsample/crams[]
downsample_strategy
max_alternate_alleles Integer (Optional)
qc_minimum_base_quality Integer
variant_index_parameter String (Optional)
emit_reference_confidence
qc_minimum_mapping_quality Integer

Steps

ID Runs Label Doc
downsample
../tools/downsample.cwl (CommandLineTool)
downsample unaligned BAM
haplotype_caller scatter GATK HaplotypeCaller over intervals
collect_wgs_metrics
../tools/collect_wgs_metrics.cwl (CommandLineTool)
collect WGS metrics

Outputs

ID Type Label Doc
gvcfs 0c0ac233da0b4e57a6215839a7df0b51[]
wgs_metrics File[]
Permalink: https://w3id.org/cwl/view/git/06d2440d115b446c299b4ce96e8812d2f8df86ec/definitions/pipelines/downsample_and_recall.cwl