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 <ymw...@gmail.com> 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 > > ------------------------------------------------------------ > ------------------ > > _______________________________________________ > Samtools-help mailing list > Samtools-help@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/samtools-help > >
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