Keep SNP's with call rate greater than 30 in VCF
I have approximately 10 samples, and I am working on identifying Runs of Homozygosity (ROH).
1) Is it necessary to merge all the samples when performing ROH analysis?
2) I'm attempting to handle missing data, but I'm confused about the usage of --geno in PLINK and --max-missing in VCFtools. What values should I use for these options if I want to retain SNPs with a call rate greater than 30%?"
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Bastien Hervé
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Smilesky •
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Smilesky •
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