Problem with Haploview loading of files from latest (Sept 15-17 2014) update to phase 3 release of 1000 Genomes data

Question

[Scott]

I am having all kinds of trouble with loading files from 1000 Genomes into Haploview. This seems to be specific to the new update (v5 just updated Sept 17 2014) of the Phase 3 "20130502" release. I can load a .ped downloaded Sept 14 2014 just fine. If I generate the same .ped today (Sept 18 2014) with the same genomic coordinates and from the same population from the 1000 Genomes VCF to PED converter, I get a fairly consistent error message even if I try different segments of the chromosome I am interested in:

"file input error on line [x], marker [y]. For any marker, an individual's genotype must be only letter or only numbers."

where x is usually somewhere in the first ten lines, and y is the last marker in the sample.

I have checked the files manually and there no not seem to be any non- ACGT characters, spaces at the end of the line before the line break, or anything unusual about the file.

Advice would be greatly appreciated.

[genogeno]

Hi, I have same problem.

Is there anybody who can help?

Thanks!

Answer 1

[Scott]

In case anyone has ran into this, it looks like it is due to the characters used for genotype calls that were not able to be made. I will update with a full explanation/ solution soon.

[Mark Ebbert]

Hey Scott, did you ever figure this out?

[Scott]

Hi Mark,

Yes. Sorry I never expanded on the last explanation. I couldn't get these files to work as they were. I had to manually edit the no calls. I ultimately ended up doing this with VCFtools instead. Were you having the same problem, or just interested?

[b.dheeraj1988]

Hi Scott,

Could you please tell me how did you fix the problem. Basically, I have a vcf file and I have converted it to PED and MAP files by vcftools. Then I tried to load it into haploview and it throws this error "For any marker, an individual's genotype must be only letters or only". I have checked the vcf file and ped file. Everything looks fine. Please let me know. Thanks in advance.