haploview to cervus
0
0
Entering edit mode
17 months ago
marion.ryan ▴ 40

I have formatted a genotype file for haploview and have now obtained the genotypes of the parents and wish to carry out parentage testing (Sheep). Any advise on converting my existing file format so it would be suitable for analysis in Cervus or any other parentage testing software, would be greatly appreciated

SNP parentage software • 392 views
ADD COMMENT
0
Entering edit mode

Hey, is Cervus still in use? Last I heard, it was released for use on Windows 95. Do you have a local copy of it? What format does it require?

ADD REPLY
0
Entering edit mode

It appears to be still in use (licenced 2014), Its not terribly good at describing the format it needs but calls it a genotype file which it describes with words, I have mine in haploview format and I am wondering if ther is a quick was of changing this format http://www.fieldgenetics.com/pages/aboutCervus_Using.jsp I am new to this so if you have suggestions for other tools for parentage testing I would be interested in your opinion

ADD REPLY
0
Entering edit mode

Please use ADD COMMENT or ADD REPLY to answer to previous reactions, as such this thread remains logically structured and easy to follow. I have now moved your reaction but as you can see it's not optimal. Adding an answer should only be used for providing a solution to the question asked.

ADD REPLY
0
Entering edit mode

Ah, they may mean the GEN ('Oxford') format, which is outlined here on PLINK2's website: https://www.cog-genomics.org/plink/1.9/formats#gen

I cannot exactly recall the HaploView format but I believe it is similar.

Unfortunately, for whatever reason when all of these genetics analysis programs were being developed, different groups decided that they needed to define their own format. This happens in many fields, though.

ADD REPLY
1
Entering edit mode

Thank you so much that is a real help, I'll just work on formatting a subset of SNPs (Haploview wants has the genotypes in one column as opposed to two) for and see if it works on that basis. I might check out Plink also. M :)

ADD REPLY

Login before adding your answer.

Traffic: 2463 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