search

fanagislab / GCE

GCE (genomic charactor estimator) is a bayes model based method to estimate the genome size, genomic repeat content and the heterozygsis rate of the sequencing sample. The estimated result can be used to design the sequencing strategy.
47 stars 5 forks source link

How to find the heterozygosity #5

Open manoharbisht1998 opened 1 year ago

manoharbisht1998 commented 1 year ago

Thank you for this tool! I have successfully run the GCE and is able to get gce.log and gce.table PFA gce.log

but now I am confused about what is heterozygosity here and how to find it.

Please help

nreid commented 10 months ago

@manoharbisht1998 I am not entirely clear on how to do this either, but I gather from the paper that you need to plug the a_1_2 statistic into equation 11 from the arXiv paper. I hope the authors will correct me if I am wrong. The number that I get out for the few cases I have tried has been similar to what I get with genomescope.

Wyclif3 commented 3 months ago

What are the parameters you used to successfully run GCE? I used ./gce -g 979524271 -f AF.freq.stat.2colum >gce.table 2>gce.log but it returned empty log and table.