freebayes for snp call in pooled samples: how do I set the parameters?

Question

[cristiana.ij.marques]

Hi everyone,

This is such a basic question coming from lack of experience. I was trying to run freebayes on 2 pools of samples (one with N=37 individuals and other with N=21). I'm using the option --pooled-discrete but I'm not sure on how to set --ploidy and --use-best-n-alleles. Can anyone help me figure out if, for diploid species, ploidy is double the number of samples you pool?

I know it's the number of genome copies per-pool but when I set --ploidy 74 (without --use-best-n-alleles) it keeps eating up all my memory and it never finishes (it's been 3 days). I'm calling only in a small region of a chromosome so it shouldn't take so long, right?

Thanks in advance :)

[ATpoint]

Also see What do the freebayes parameters --pooled-continuous/--pooled-discrete mean?. Ploidy is alleles per sample I guess not the sum of it, so 2 for diploid organisms.

Answer 1

[ross_whetten]

According to the Freebayes documentation, with the --pooled-continuous option " When running with high --ploidy settings, it may be required to set --use-best-n-alleles to a low number to limit memory usage." Even a small region of a chromosome may take too long or use too much RAM given ploidy 74 and no limit on the number of alternative alleles.