Ahhh, sorry Wolfgang, this IS the right forum. I was answering a slew of
igv-help emails and thought this was one of them.
On Mon, Nov 7, 2016 at 7:22 AM, Thomas W. Blackwell <tbla...@umich.edu>
wrote:
> 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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