Wolfgang -
If I understand the question correctly, you want to convert a
.vcf file to an alternate format in which the genotypes for one
individual at multiple sites are all on one row in the file,
rather than in one column as in .vcf. This is ".ped and .map"
format. I think 'plink' software (among others) will convert
.vcf to .ped and .map format.
- tom blackwell -
On Mon, 7 Nov 2016, Rumpf, Wolfgang wrote:
> I'm a total n00b when it comes to Samtools so forgive me for the n00b
> questions. I have received several (10 or so) .var.flt.vcf files from a
> collaborator and would like to convert them to something resembling a
> sequence alignment, where each file simply gives me a "sequence" comprised of
> the measured SNPs for that individual. I'm not concerned with retaining
> metadata/positional information, since I can always recover that from the
> original file - I just want to be able to compare all of these in a single
> view. Any suggestions on the easiest way of doing this? Thanks in advance!
>
> - Wolfgang --?
>
>
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