modules/stitch
STITCH is an R program for reference panel free, read aware, low coverage sequencing genotype imputation. STITCH runs on a set of samples with sequencing reads in BAM format, as well as a list of positions to genotype, and outputs imputed genotypes in VCF format.
Description
STITCH is an R program for reference panel free, read aware, low coverage sequencing genotype imputation. STITCH runs on a set of samples with sequencing reads in BAM format, as well as a list of positions to genotype, and outputs imputed genotypes in VCF format.
Input
Groovy Map containing information about the set of positions to run the imputation over
e.g. [ id:'test' ]
Tab-separated file describing the variable positions to be used for imputation. Refer to the documentation for the --posfile argument of STITCH for more information.
*.tsv Folder of pre-generated input RData objects used when STITCH is called with the --regenerateInput FALSE flag. It is generated by running STITCH with the --generateInputOnly TRUE flag.
input Folder of pre-generated input RData objects used when STITCH is called with the --regenerateInput FALSE flag. It is generated by running STITCH with the --generateInputOnly TRUE flag.
RData Name of the chromosome to impute. Should match a chromosome name in the reference genome.
Number of ancestral haplotypes to use for imputation. Refer to the documentation for the --K argument of STITCH for more information.
Number of generations since founding of the population to use for imputation. Refer to the documentation for the --nGen argument of STITCH for more information.
Text file with the path to the cram files to use in imputation, one per line. Since the cram files are staged to the working directory for the process, this file should just contain the file names without any pre-pending path.
*.txt Output
Folder of pre-generated input RData objects used when STITCH is called with the --regenerateInput FALSE flag. It is generated by running STITCH with the --generateInputOnly TRUE flag.
input Folder of pre-generated input RData objects used when STITCH is called with the --regenerateInput FALSE flag. It is generated by running STITCH with the --generateInputOnly TRUE flag.
RData Folder containing plots produced by STITCH during imputation. Which plots are produced depends on the command-line arguments passed to STITCH.
plots Imputed genotype calls for the positions in posfile, in vcf format. This is the default output.
.vcf.gz Imputed genotype calls for the positions in posfile, in vcf format. This is the produced if --output_format bgen is specified.
.bgen 