Workflow: LodSeq

Fetched 2022-05-29 05:10:00 GMT

LodSeq performs the genetic linkage analysis across families, by computing lod-scores given a gvcf file and a related tfam pedigree file.

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Inputs

ID Type Title Doc
vcf File
tfam File
dom_model File
rec_model File
out_prefix String
chromosomes String[]
genetic_maps Directory
lod_threshold Float

Steps

ID Runs Label Doc
prepareVCF
prepareVCF.cwl (CommandLineTool)
prepareVCF

prepareVCF get .ped and .map files from .vcf and .tfam files and check that all input files and directories exist

mergeResults
merge.cwl (CommandLineTool)
splitByChrom
splitByChrom.cwl (CommandLineTool)
splitByChrom

splitByChrom split files (.ped .map) by chromosome

prepareGeneticMaps
prepareGeneticMaps.cwl (CommandLineTool)
prepareGeneticMaps

prepareGeneticMaps removes header from genetic map file(s)

runMultiPointMerlin
runMultiPointMerlin.cwl (CommandLineTool)
runMultiPointMerlin

runMultiPointMerlin run multi point merlin analysis

runSinglePointMerlin
runSinglePointMerlin.cwl (CommandLineTool)
runSinglePointMerlin

runSinglePointMerlin run single point merlin analysis

prepareMultiPointFiles
prepareMultiPointFiles.cwl (CommandLineTool)
prepareMultiPointFiles

prepareMultiPointFiles prepare multipoint merlin analysis inputs

prepareSinglePointFiles
prepareSinglePointFiles.cwl (CommandLineTool)
prepareSinglePointFiles

prepareSinglePointFiles prepare single point merlin analysis inputs

Outputs

ID Type Label Doc
out_dir Directory
out_dir_mr Directory
out_dir_pgm Directory[]
out_dir_pmf Directory[]
out_dir_psf Directory[]
out_dir_rmm Directory[]
out_dir_rsm Directory[]
out_dir_sbc Directory[]
Permalink: https://w3id.org/cwl/view/git/c40ac3f30ea811bffbcf50c5a315212c8673db19/workflows/cwltoil/lodseq.cwl