Question: Plink - resolving heterozygous haploid genotypes if an XY chromosome is already assigned in GWAS
0
gravatar for Vincent Laufer
2.7 years ago by
Vincent Laufer1.0k
United States
Vincent Laufer1.0k wrote:

There is a previous biostars post that deals with the use of plink2's --split-x flag to handle cases when a large number of markers need to be moved to XY (https://www.biostars.org/p/98211/), or chr25 in plink coding.

However, my case is a bit different.

Although the data that came from the sequencing center already appears to have a chr25, I am still getting the error:

180461 heterozygous haploid genotypes; set to missing
Writing list of heterozygous haploid genotypes to [ file.hh ]
44121 SNPs with no founder genotypes observed

However, running plink2 gives:

4221792 variants and 191 people pass filters and QC.
Among remaining phenotypes, 191 are cases and 0 are controls.
Error: --split-x cannot be used when the dataset already contains an XY region.

So, I did a little digging and I found that nearly all of the SNPs that end up in the .hh file are on either chrX, chrY, chrXY, or chrM (corresponding to plink chr23-26).

Further, it seems that although many are at the beginning and end of chrX, others are in discrete regions, and some are on chr24 (Y) or chr26 (M), and there are a few others as well.

I am wondering now what my next steps should be or what the options for next steps are and why. Thank you very much for your help.

plink gwas • 1.7k views
ADD COMMENTlink modified 2.6 years ago by dgrover610 • written 2.7 years ago by Vincent Laufer1.0k
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: 1518 users visited in the last hour