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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