[Samtools-help] mpileup result in indel containing SNP

[Hung Chih-M. <ym...@gm...>]

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