9.4 posfile

This format creates a file containing information about SNP positions. It is needed as an input (argument posfile) for the imputation tool STITCH. The file is tab-seperated with four columns: chromosome, position, reference base, alternative base, and with one row per locus. If STITCH is run on one chromosome only, the option keepChromosomes can be used to specify the chromosome to keep while converting the VCF. ” is a bit unclear to read, I would suggest to phrase it instead as “The file is tab-separated with four columns: chromosome, position, reference base and alternative base, with each row representing a single locus. If STITCH is run on a single chromosome, use keepChromosomes to specify which chromosome to retain when converting the VCF. Here is an example for four loci:

chr1	1	A	C
chr1	2	G	T
chr1	3	C	A
chr2	5	T	A