Joining Clinvar with variant data using sql
0
0
Entering edit mode
6.1 years ago
iCode • 0

I want to join my variant data (from 23andMe) with clinvar and I see people Join them differently. Specifically, these are the join on clauses

            sample.chromosome = clinvar.chromosome
    AND sample.startposition = clinvar.startposition - 1
    AND sample.endposition = clinvar.endposition
    AND sample.referenceallele = clinvar.referenceallele

that was used in this blog: https://aws.amazon.com/blogs/big-data/interactive-analysis-of-genomic-datasets-using-amazon-athena/

As you see, clinvar.startposition has a minus 1 (clinvar.startposition - 1) but I am seeing others are not doing so and just say

  ...
  AND sample.startposition = clinvar.startposition
  ...

What is the proper way to join my variants with clinvar. should I have that minus 1 on the startposition or not? and why?

clinvar variant 23andme • 1.5k views
ADD COMMENT
0
Entering edit mode

it depends how data have been inserted. Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems

ADD REPLY
0
Entering edit mode

Thank you. Would you have happened to know what Coordinate Systems 23andMe api data and Clinvar data are in?

ADD REPLY

Login before adding your answer.

Traffic: 3000 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6