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abyzovlab / vcf2diploid

personal genome constructor
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Specifying which is the paternal/maternal allele #2

Open dylkot opened 9 years ago

dylkot commented 9 years ago

In a VCF file with a genotype entry 1|0, does vcf2diploid take the left entry as the paternal allele and right value as the maternal allele? I can't seem to find this in the documentation anywhere. Thus in the above example, the paternal allele would be alternate and the maternal allele would be reference.

Thanks!

abyzov commented 9 years ago

Yes, this is correct -- "paternal|maternal". This is the convention used by the 1000 Genomes Project.

dylkot commented 9 years ago

Thanks! I appreciate the response.