Output Files

The various output files produced by snps are detailed below. Output files are saved in the output directory, which is defined at the instantiation of a SNPs object.

Save SNPs

SNPs can be saved with SNPs.save. By default, one tab-separated .txt or .vcf file (vcf=True) is output when SNPs are saved. If comma is specified as the separator (sep=","), the default extension is .csv.

The content of non-VCF files (after comment lines, which start with #) is as follows:

Column Description
rsid SNP ID
chromosome Chromosome of SNP
position Position of SNP
genotype Genotype of SNP

When filename is not specified, default filenames are used as described below.


<source>_<assembly>.txt / <source>_<assembly>.csv

Where source is the detected source(s) of SNPs data and assembly is the assembly of the SNPs being saved.