Intermediate .RData files to outputs VCF format

[lanxianmei]

Hi,

I had deleted my imputation input bam files and the output VCF format files. Can I produce the output vcf files from the intermediate .RData files and how?

best

[rwdavies]

Hi,

You should be able to. So for example if this was your original run

    STITCH(
        chr = "chr5",
        bamlist = data_package$bamlist,
        posfile = data_package$posfile,
        outputdir = outputdir,
        K = 2,
        nGen = 100
    )

Then you can re-run with no bams using something like this

    STITCH(
        chr = "chr5",
        originalRegionName = "chr5",        
        regenerateInput = FALSE,
        regenerateInputWithDefaultValues = TRUE,
        posfile = data_package$posfile,
        outputdir = outputdir,
        K = 2,
        nGen = 100
    )

Alternatively if you used regionStart etc then something like

# original call
   STITCH(
        chr = "chr5",
        regionStart = 10,
        regionEnd = 30,
        buffer = 5,
        bamlist = data_package$bamlist,
        posfile = data_package$posfile,
        outputdir = outputdir,
        K = 2,
        nGen = 100,
    )

# re-run with no bams
    STITCH(
        chr = "chr5",
        originalRegionName = "chr5.10.30",        
        regenerateInput = FALSE,
        regionStart = 10,
        regionEnd = 30,
        buffer = 5,
        posfile = data_package$posfile,
        outputdir = outputdir,
        K = 2,
        nGen = 100
    )

[lanxianmei]

Hi rwdavies,

Thank you for your help and happy to see it work for me.

best