I fear you have misunderstood something. Yes, VCFs are typically generated from BAM files, but BAM files are *not* generated from fasta files. BAMs are generated from a sequencing experiment where fastq files are aligned to a reference sequence.
I don't think this is the right forum for your query. Try biostars.org and explain what biological question it is you're trying to answer. Regards, Chris From: Vanessa Oliveira Date: Friday, 22 May 2015 15:19 To: "[email protected]", samtools Subject: Re: [Samtools-help] how to convert fasta to bam format >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 >> >> > > > > > The University of Dundee is a registered Scottish Charity, No: SC015096 ------------------------------------------------------------------------------ One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applications Performance metrics, stats and reports that give you Actionable Insights Deep dive visibility with transaction tracing using APM Insight. http://ad.doubleclick.net/ddm/clk/290420510;117567292;y _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
