I understood the only way to go from fasta to VCF is creating bam file.
Is there another way?
2015-05-22 10:14 GMT-04:00 Peter Cock <[email protected]>:
> Hi Vanessa,
>
> What do you mean by ped/map?
>
> BAM files are normally for storing the alignment of many (e.g.
> millions) of short sequencing reads against many reference
> sequences (e.g. 12 chromosomes, or 10000 contigs).
>
> Once you have a BAM file, then yes, you can look for SNPs etc
> using VCF (variant call format).
>
> Peter
>
> P.S. You replied to me only, not the mailing list. You can include
> this reply if you want to return this discussion to the public list.
>
> On Fri, May 22, 2015 at 3:04 PM, Vanessa Oliveira <[email protected]>
> wrote:
> > Hi Peter,
> >
> > These sequences were downloaded from data bases. I will use them as
> > reference panel and I need to have the file as ped/map. Is that possible
> to
> > convert it through fasta --> bam; bam --> VCF in samttools and bcftools?
> >
> > Many thanks,
> >
> > Cheers,
> >
> > Vanessa
> >
> > 2015-05-22 5:38 GMT-04:00 Peter Cock <[email protected]>:
> >
> >> On Thu, May 21, 2015 at 9:16 PM, Vanessa Oliveira <[email protected]
> >
> >> wrote:
> >> > Hi,
> >> >
> >> > I have a fasta file with mtDNA sequences. I want to convert them to
> bam
> >> > file.
> >> >
> >>
> >> Why? I think you are asking the wrong question.
> >>
> >> If your FASTA file is complete mtDNA sequences (e.g. from different
> >> organsism or samples), you might want to look at multiple sequence
> >> alignment.
> >>
> >> If your FASTA file is fragments of mtDNA sequence from the same
> >> organism/sample, then you might want to look at *aligning* these
> >> sequences to a known reference mtDNA sequence (where the
> >> alignment would be a SAM or BAM file).
> >>
> >> Peter
> >
> >
>
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