Hi all,
I am trying to calculate homozygosity by loci from my SNPs data according to Aparicio et al., 2006 https://pubmed.ncbi.nlm.nih.gov/17107491/. I have a vcf file of 38,140 SNPs with 60 individuals. Does it sounds sensible to use Cernicalin? It seems that the current Cernicalin version can only handle 30 loci, 200 alleles per locus, and 1200 individuals. There are also two R packages developed for calculating homozygosity indexes,
rhh (Alho et al., 2010. https://onlinelibrary.wiley.com/doi/full/10.1111/j.1755-0998.2010.02830.x) and Genhet (Coulon 2010. https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1755-0998.2009.02731.x). However, it's not clear how the input files were prepared. The genotype information looks different from different datasets. Can the genotype information be represented as GT format extracted directly from the vcf file?
Thanks,
Jia
Maybe you could give a try to Genepop (https://genepop.curtin.edu.au/) or Arlequin (http://cmpg.unibe.ch/software/arlequin35/) and do the file conversion with PGDSpider (http://www.cmpg.unibe.ch/software/PGDSpider/)
Thanks Jose Alberto Lopez-Aleman and Anna Wolc for your replies and insightful suggestions, they are really helpful. Will check out the methods you mentioned. I am firstly trying to use R package "genhet" by converting vcf file to structure using PGDSpider because they this package was developed for HL calculation. On the way to figure out the input file format.
p.s., just for clarification, it is not possible to calculate HL with Cernicalin for such a large dataset.
Hi Jia:
You can find examples for the Genhet package here:
http://www.aureliecoulon.net/research/ac-computer-programs.html
But like Dr. Anna Wolc, I highly recommend plink to calculate homozygosity. Perhaps you also want to check their page:
https://www.cog-genomics.org/plink/1.9/ibd
- Badges
- Science topic
- Similar topics
- Statistics
- Survey