HaploView error messages for HapMap3 and 1000Genomes phase 3 data!

Question

[mdgallagher71]

Please help! When I try to download YRI HapMap3 SNP genotype data and open it in HaploView, I get an error that says HapMap data format error: NA18776

When I try to circumvent this problem using 1000 Genomes phase 3 data, I get an error message saying that line 219 has more than two alleles.

Anyone have any ideas?

Thanks!

Answer 1

[Adam]

The Phase 3 data includes many multiallelic sites. Such sites aren't supported by haploview, and would therefore need to be removed in order to view in haploview. You could do this using, for example, vcftools with the --max-alleles option.

[mdgallagher71]

Ok thanks - when looking at 1000 Genomes Phase 1 YRI data, however, I also run into problems. I'm not sure how to use vcftools, but when I try to download the Phase 1 YRI data, I get an error message saying "Broken VCF header, no column names?"