mpileup on haploid samples

[agc]

Hi,

When running `samtools mpileup` with no parameters , it says that mpileup assumes diploid individuals. I'm working with haploid samples - does that mean I have to find a different SNP / Indel caller? Or is there a way to specify haploid samples?

Thanks.

[lh3]

If you are working on a single sample, I think the best practice is to assume the sample is diploid. You filter out heterozygous calls afterwards. Frequently hets indicate copy number changes. If you force to call a hom, you will get an error. Read the maq paper. Three clustered hets indicate an extra copy of tRNA.