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$pacbamByChromFolder)`
Structure of folders is correct and so the generated files. Any idea?
Thanks!
Hi there,
I am having issues in calling the "callsnvs" command. Error is:
Error in names(snvs) <- c("chr", "pos", "ref", "alt", "A", "C", "G", "T", : 'names' attribute [15] must be the same length as the vector [11]I succeeded in all steps except this one. I write the commands I used here, so maybe someone can suggest a solution:
split_pacbam_bychrom(targetbed = args$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!