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.
SNPs.save
<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.