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Old 01-06-2015, 06:27 AM   #1
huma Asif
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Location: Japan

Join Date: Oct 2010
Posts: 53
Default vcf_to_ped_convert.pl

Dear All,
i need your help in visualizing 1000 genome data in haploview
when I upload the file on Haploview version 4.2 i get this error
more than two alleles at marker 300
Any help would be highly appreciated
which vcf to ped converter is better for biallelic sites.as 1000 genomes vcf to ped converter work for multiallelic site

Last edited by huma Asif; 01-07-2015 at 02:45 AM.
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Old 08-07-2015, 01:08 AM   #2
sumsuh
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Location: Sweden

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"more than two alleles at marker 300"

I got the same problem working with my data and when I checked the data I realized I made a mistake while recoding my data. The program can only handle biallelic markers:

0=missing
1=A, 2=C, 3=G, 4=T

If the data in the columns for marker 300 has more than 2 alleles (e.g. 1,2 and 3) this error will occur.

I hope this helps. I'm new at this so I can not answer your question about what converter is best.
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