Dear all,
I got a sequencing result file (already variant called) without extension name recently. The column of the file is as following:
chr pos ref.allele id1 id2 ... number.of.sample.without.missing variant.type alt.allele
chr1 00000 A A/A A/A ... 302 SNP G
chr2 99999 G G/T G/G ... 300 SNP T
...
However, i never met this kind of format before, so could any one please give me some idea that what kind of format is this file?
Thank you very much!
Your sincerely,
henry
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m338102001 •
Looks like a vcf file; not sure from where the below column came:
number.of.sample.without.missing variant.type alt.allele
Or probably the genotype File Format
For details, check this link.
No, it is not a VCF.
The VCF is quite-well defined and this does not fit.
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Have you tried to contact the person who provided the file? It might be that the file is in a custom tabular data format unique to the provider pipeline?