Question: inPHAP graphical genotype visualization: metadata file format
0
gravatar for Dtriumph
2.5 years ago by
Dtriumph30
Dtriumph30 wrote:

Hi ,

I'm trying to create graphical genotypes using my unphased SNP data using inPHAP software. The software requires two input files, 1). hapmap file in vcf format and 2). tab delimited metadata text file including related information for grouping the individuals. I could load both files but my metadata information is not recognized by the program and it's shown as red crosses instead of colored bars. Can anyone tell me what is wrong with my metadata input file?

Below is the format of my metadata file,

Individual_ID Trait Population 10001 AL 1 10002 AC 1 10003 AL 2 10004 AL 2

Thank you!

GUI snap shot

ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by Dtriumph30
2
gravatar for Dtriumph
2.5 years ago by
Dtriumph30
Dtriumph30 wrote:

Just wanted to post an update for the benefit of anyone who comes across the same issue, as I resolved this problem after a bit of struggle. The individual IDs in the metadata file should be formatted as following,

Individual_ID Trait Population 10001_10001 AL 1 10002_10002 AC 1 10003_10003 AL 2 10004 AL 2

For an example, if the Individual_ID on hapmap file is 10001, the Individual_ID on metadata file for the same individual should be 10001_10001.

Thanks! D

ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by Dtriumph30
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1225 users visited in the last hour