Genome-wide heterozygosity
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4 months ago
gubrins ▴ 130

Heys,

I want to calculate genome-wide heterozygosity for a couple of samples I have. I have been looking in internet but I just find theoretical definitions of how you should do it, rather than practical examples. Is there any software or custom batch script already optimized? I have bam or vcf files!

Thanks in advance!

heterozygosity genome • 755 views
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snippy can assist in reference-based genome-wide heterozygosity analysis but it needs fastq files (raw reads).

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Hi @gubrins, did you every get anywhere with this? Did you use snippy, as suggested by @MSRS, or another tool? Looking at doing the same thing and wondering how you went about it. Cheers!

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Heys clinnaeus , I didn't receive the notification from @MSRS so I didn't try it! However, I would prefer to find a way to calculate the heterozygosity through my complete vcf file, because as I did the snps calling with GATK, I imagine is going to be more realible and at the same time is the file I will use for other analyses. Let's keep in touch and try to solve this together if you want. From which type of file do you wanna calculate the heterozygosity?

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Check this paper!

https://onlinelibrary.wiley.com/doi/full/10.1111/mec.16184?campaign=wolacceptedarticle

I'm on a course, so I'll try next week and I will let you know if works with the softwares they mention. Good luck!

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Hi gubrins - thanks so much for replying! I'm definitely keen to try to work together. Sorry it took so long for me to reply, I didn't get a notification for your messages. I'm also interested in calculating the hetz from the vcf if possible - I've been thinking of using ROHAN to try to estimate global rates of hetz but haven't had time to implement yet. I'll have a go this week and let you know how it goes, and we can compare. Shall we connect via Twitter?

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good to me, I'm also gubrins in twitter!

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