User: nschaefer

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nschaefer20
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Posts by nschaefer

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Comment: C: VCF format for phased data
... OK, so the phasing is with the line(s) before rather than after the |. I wish that had been made explicit in the 1000Genomes page.   Thanks again ...
written 4.6 years ago by nschaefer20
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Comment: C: VCF format for phased data
... Thanks Chris for the link. Whilst it may not have answered the specific question, it was very interesting for my broader goals viz; imputing/interpolating values for all alleles in my 23&Me phased results (1M positions) using larger databases such as 1000Genomes and beyond.  ...
written 4.6 years ago by nschaefer20
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Comment: C: VCF format for phased data
... From what you're saying the position of the value wrt | is significant. So in your example the last three positions on the left of | implies they are ALT and on the same chromosome whilst to the right of | the values are REF and on the other chromosome. However as the first position is not phased is ...
written 4.6 years ago by nschaefer20
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VCF format for phased data
... Despite the detailed explanation of VCF format on the 1000Genomes site, it is still not clear to me how the data should be interpreted with respect to sample results. CHROM POS     ID        REF    ALT     QUAL FILTER INFO                                    FORMAT           NA00002 20     14370   ...
vcf 1000 genomes phased written 4.6 years ago by nschaefer20 • updated 22 months ago by Biostar ♦♦ 20

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