Skip to content

Commit 4283e4a

Browse files
nevromestschiff
andauthored
Update genotype_data.md
Co-authored-by: Stephan Schiffels <stephan_schiffels@eva.mpg.de>
1 parent 5e2164d commit 4283e4a

1 file changed

Lines changed: 1 addition & 1 deletion

File tree

genotype_data.md

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -14,7 +14,7 @@ The PLINK file format is a well specified, storage efficient data type compatibl
1414

1515
To make VCF files fully convertible to PLINK and EIGENSTRAT, they MUST be biallelic and contain only genotypes coded as `0/0`, `0/1`, `1/1`, `./.`. Furthermore, they CAN encode group names and genetic sex for all samples through special header fields `##group_names=name1,name2,...` and `##genetic_sex=F,U,M,...`, respectively. If these fields are not present, then group names are assumed to be "unknown" and genetic sex "U" (unknown) for all samples.
1616

17-
For all of these formats the large genotype data files to store SNP definitions and values can be stored in gzipped form (`*.gz`).
17+
For all of these formats the genotype and SNP-definition files can be stored in gzipped form (`*.gz`), i.e.: `*.bed.gz`, `*.geno.gz`, `*.bim.gz`, `*.snp.gz`, `*.vcf.gz`, but note that `*.fam` and `*.ind` files always must remain unzipped.
1818

1919
The `genotypeData` field in the `POSEIDON.yml` file documents in which format the data for a package is stored and the relative paths to the respective files.
2020

0 commit comments

Comments
 (0)