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=== Profile Mendelian Errors ===
Profile Mendelian errors
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#profile mendelian errors found in vt.genotypes.bcf, generate [[media:mendel.pdf|tables]] in the directory mendel, requires pdflatex.
vt profile_mendelian vt.genotypes.bcf -p trios.ped -x mendel
pedigree file format is described in [http://csg.sph.umich.edu//abecasis/merlin/tour/input_files.html here]
#this is a sample output for mendelian error profiling.
#R and A stand for reference and alternate allele respectively.
#Error% - mendelian error (confounded with de novo mutation)
#HomHet - Homozygous-Heterozygous genotype ratios
#Het% - proportion of hets
Mendelian Errors <br>
Father Mother R/R R/A A/A Error(%) HomHet Het(%)
R/R R/R 14889 210 38 1.64 nan nan
R/R R/A 3403 3497 74 1.06 0.97 50.68
R/R A/A 176 1482 155 18.26 nan nan
R/A R/R 3665 3652 68 0.92 1.00 49.91
R/A R/A 1015 3151 990 0.00 0.64 61.11
R/A A/A 43 1300 1401 1.57 1.08 48.13
A/A R/R 172 1365 147 18.94 nan nan
A/A R/A 47 1164 1183 1.96 1.02 49.60
A/A A/A 20 78 5637 1.71 nan nan <br>
Parental R/R R/A A/A Error(%) HomHet Het(%)
R/R R/R 14889 210 38 1.64 nan nan
R/R R/A 7068 7149 142 0.99 0.99 50.28
R/R A/A 348 2847 302 18.59 nan nan
R/A R/A 1015 3151 990 0.00 0.64 61.11
R/A A/A 90 2464 2584 1.75 1.05 48.81
A/A A/A 20 78 5637 1.71 nan nan <br>
Parental R/R R/A A/A Error(%) HomHet Het(%)
HOM HOM 14909 288 5675 1.66 nan nan
HOM HET 7158 9613 2726 1.19 1.00 49.90
HET HET 1015 3151 990 0.00 0.64 61.11
HOMREF HOMALT 348 2847 302 18.59 nan nan <br>
total mendelian error : 2.505%
no. of trios : 2
no. of variants : 25346
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profile_mendelian v0.5
usage : vt profile_mendelian [options] <in.vcf>
options : -q minimum genotype quality
-d minimum depth
-r reference sequence fasta file []
-x output latex directory []
-p pedigree file
-I file containing list of intervals []
-i intervals
-? displays help
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=== Profile SNPs ===
=== Profile SNPs ===
