![]() You can see that some individuals have as high as 99.6% missing data. INDV N_DATA N_GENOTYPES_FILTERED N_MISSğ_MISS We can do this by assessing individual levels of missing data. The next step is to get rid of individuals that did not sequence well. Right now, the maximum error rate for our VCF file because of genotypes less than 5 reads is less than 5%. The total SCORCHED EARTH error rate is 0.129149100834. WHAT IF ALL LOW DEPTH HOMOZYGOTE GENOTYPES ARE ERRORS? 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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