Re: [Samtools-help] cns2snp

[Richard D. <rd...@sa...>]

Yes. pileup2vcf would be the right thing, as a program external to 
samtools.  Richard

Heng Li wrote:
> On Wed, Aug 26, 2009 at 01:55:22PM +0100, Nava Whiteford wrote:
>   
>> Is there a samtools equivalent of the maq cns2snp command?
>>     
>
> No, there is no equivalence. Nonetheless, the pileup output is in plain
> text. It would not be hard to get information with scripting languages.
>
>   
>> Some kind of pileup2snp perhaps?
>>     
>
> Maybe we need a pileup2vcf. VCF (variant call format) will be a new
> standard for storing SNP calling.
>
> Heng
>
>   
>> Nav
>>
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