![]() ![]() Total genotypes not counting missing data 2380094 Potential genotyping errors from genotypes from only 5 reads range from 2493 to 18914Ĥ0 number of individuals and 78434 equals 3137360 total genotypes Potential genotyping errors from genotypes from only 4 reads range from 6230 to 31502.04 ![]() Potential genotyping errors from genotypes from only 3 reads range from 15986 to 53714.22 Potential genotyping errors from genotypes from only 2 reads range from 0 to 0.0 Potential genotyping errors from genotypes from only 1 read range from 0 to 0.0 It report a low range, based on a 50% binomial probability of observing the second allele in a heterozygote and a high range based on a 25% probability. This script counts the number of potential genotyping errors due to low read depth We are going to only keep variants that have been successfully genotyped inĥ0% of individuals, a minimum quality score of 30, and a minor allele count of 3. To make this file more manageable, let’s start by applying three step filter. This raw.vcf file is going to have a lot of erroneous variant calls and a lot of variants that are only present in one individual. I find it much more useful to use version 0.1.11, since it has more useful filtering commands (I think). This program has a binary executableĪnd has several perl scripts as well that are useful for filtering. ![]() To start, we are going to use the program VCFtools () to filter our vcf file. 1 jpuritz users 137209 Mar 6 14:30 stats.out 1 jpuritz users 6804314 Mar 6 14:49 reference.fasta ![]()
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