search

luntergroup / octopus

Bayesian haplotype-based mutation calling
MIT License
302 stars 38 forks source link

Settings for highly homozygous GBS data. #135

Closed DiDeoxy closed 4 years ago

DiDeoxy commented 4 years ago

Hi,

I am working with GBS Barley data, barley is an inbred crop species and is therefor highly homozygous.

Do you have any recommendations for the settings for Octopus for such data?

Thanks,

Max H.

dancooke commented 4 years ago

Hi Max,

There's no inbreeding parameter in Octopus currently. What's the diversity like? You could adjust the --snp-heterozygosity and --indel-heterozygosity parameters if heterozygosity is far from the defaults. If heterozygosity is really high then you might need to consider adjusting other parameters like --max-haplotypes.

My other advice, in the absence of some good quality truth data, would be to call a sample region and use the --bamout option to get realigned reads. You can then view these in IGV coloured and split by the HP tag. This is a really nice way of visually validating what was called because ideally you should be seeing two clean haploid haplotypes. See this wiki page for more details.

Dan

dancooke commented 4 years ago

Closing this - please re-open if any further help needed.