Skip to content

Error in callsnvs command #5

@wynstep

Description

@wynstep

Hi there,
I am having issues in calling the "callsnvs" command. Error is:
Error in names(snvs) <- c("chr", "pos", "ref", "alt", "A", "C", "G", "T", : 'names' attribute [15] must be the same length as the vector [11]

I succeeded in all steps except this one. I write the commands I used here, so maybe someone can suggest a solution:

split_pacbam_bychrom(targetbed = args$regions, pacbamfolder = args$pacbamFolder, pacbamfolder_bychrom = args$pacbamByChromFolder)

perBaseErrorModel <- compute_pbem(sample.info.file = args$sampleInfo, targetbed = args$regions, outdir = args$outDir, pacbamfolder_bychrom = args$pacbamByChromFolder)

allelicFractionThresholds <- compute_afthreshold(outdir = args$outDir, pbem_dir = file.path(args$outDir,"BaseErrorModel"))

snvs <- callsnvs(sample.info.file = args$sampleInfo, controls_dir = file.path(args$outDir,"Controls"), pbem_dir = file.path(args$outDir,"BaseErrorModel"), detection.specificity = 0.995, replicas = 10, outdir = args$outDir, outdir.calls.name = "SNVs", targetbed = args$regions, pacbamfolder_bychrom = args$pacbamByChromFolder)`

Structure of folders is correct and so the generated files. Any idea?

Thanks!

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions