Single nucleotide polymorphism (SNP) discovery in polyploid

[ramouz87]

Hi,
I would like to find SNP in polyploid organism(having more than 2 chromosomes), is there any SNP discovery tool that can handel that ?
If not, anyone know how to compute SNP confidence score from concensus call in this case ?
Thanks in adavnce for your suggestions
Best,
Ramzi

[nilshomer]

Hi,
I would like to find SNP in polyploid organism(having more than 2 chromosomes), is there any SNP discovery tool that can handel that ?
If not, anyone know how to compute SNP confidence score from concensus call in this case ?
Thanks in adavnce for your suggestions
Best,
Ramzi

Not too sure, but what about the "-N" option in "samtools pileup"? I say I am not too sure since I am not sure how SNPs with one out of N copies will be reported (N>2).