Re: [Samtools-help] mpileup result in indel containing SNP

[Colin H. <co...@no...>]

Hi,

I expect that you need to use a reference that doesn't have IUPAC ambiguous
codes like R in it, at least for the mpileup.

We often use ambiguous codes in the reference for alignment but not for
variant calling.

Kind Regards, Colin

On 14 September 2016 at 17:01, Hung Chih-Ming <ym...@gm...> wrote:

> Hi,
>
> When I use samtools mpileup to call variants, I found the some indels
> contain SNP sites (or genotypes) in the resulted VCF file.
> For example, a indel show GRAT and G for REF and ALT, respectively.  So,
> the "R" is the REF is a SNP (or genotype) inside indel.
>
> How can I use samtools to call indels without SNP inside the indels?
>
> Thanks,
>
> Chih-Ming
>
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