Re: [Samtools-help] how to convert fasta to bam format

[Christian C. (Staff) <C....@du...>]

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:  "p.j...@go...", 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 <p.j...@go...>:
>
>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 <van...@gm...> 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 <p.j...@go...>:
>>
>>> On Thu, May 21, 2015 at 9:16 PM, Vanessa Oliveira <van...@gm...>
>>> 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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