Re: [Samtools-help] second allele filter

[Christian C. <C....@du...>]

That's a good question. I'd be interested in the answer too.

I use GATK for variant calling, but it doesn't give this information
either.
Cheers,

Chris



On 13/08/2013 00:58, "Ruobai (Rebecca) Sun" <ru...@uc...> wrote:

>Hi All,
>
>
>I used samtools mpilup default parameters to call the SNPs. I got the one
>SNP as follows,
>
>Chr4    10143640    .    A    C,T    219    .
>DP=59;VDB=0.0392;AF1=1;AC1=2;DP4=0,0,27,30;MQ=51;FQ=-196    GT:PL:GQ
>1/1:252,169,0,245,143,242:99
>
>
>I checked this SNP in IGV, there is only one base (high quality) supports
>second allele "T". It seems odd to me that 1 out of 27 reads is
>considered a valid SNP. How can I filter out the second allele? Can I set
>any parameters in samtools mpilup command? If
> only based on VCF information, how can I know only one base support "T"?
>What information in VCF could be used to filter out second allele with
>low base support, only call the SNP with A->C changed.
>
>
>Thank you for your help.
>
>
>Rebecca


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