/23andMe-SNPs-Indexer

Utility program to index 23andMe's translation files from SNP id to chromosomal position.

Primary LanguagePython

Utility program to index 23andMe's SNPs data

Dependency

This script requires pyasm. Simply pip install pysam will do the job.

Usage

  • You will need to download 23andMe's file which contains the translation between SNP id and corresponding chromosome and chromosomal position.
  • Here's how you MIGHT do it
# download file from 23andMe
$ wget https://api.23andme.com/res/txt/snps.data -O snps.txt
# index it
$ ./index_snps snps.txt snps.sorted.txt
  • After using commands above, you will have three new files in the directory you issued the commands -- snps.sorted.txt, snps.sorted.gz, snps.sorted.gz.tbi. snps.sorted.txt is the sorted csv file containing the snps (without headers). snps.sorted.gz and snps.sorted.gz.tbi are tabix-compressed files of snps.sorted.txt.