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