Add hapmap format to genotype matrix downloads - Githubissues

UofS-Pulse-Binfo / nd_genotypes

Drupal/Tripal: Tripal interface for Chado Natural Diversity Genotypic data.

https://nd-genotypes.readthedocs.io/en/latest/index.html

GNU General Public License v2.0

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Add hapmap format to genotype matrix downloads #36

Closed laceysanderson closed 5 years ago

laceysanderson commented 5 years ago

[x] I feel this PR is ready to be merged.

Documentation:

[x] My code follows the code style of this project.
[ ] My change requires a change to the documentation.
[ ] I have updated the documentation accordingly.

Description

This PR adds the Hapmap format as a download options for the genotype matrix. The hapmap is described as Screen Shot 2019-05-21 at 6 15 54 PM Source

Testing?

[ ] I tested on a generic Tripal Site
[x] I tested on a KnowPulse Clone
[ ] This PR includes automated testing

On this branch

Go to the genotype matrix
Filter using various combinations & submit
Click on HAPMAP
Run tripal job
Check the resulting data follows the format and matches the expected data.

NOTE: This format does not support indels, which are untested with the genotype matrix in general.

Jiu9Shen commented 5 years ago

Screenshot from 2019-05-23 15-27-41

Jiu9Shen commented 5 years ago

The header of this hapmap file:
rs# alleles chrom pos strand assembly# center protLSID assayLSID panel QCcode "CDC Robin AGL" "ILL 8010 AGL"