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| </div> | | </div> |
| </div> | | </div> |
| + | |
| + | === Profile Mendelian Errors === |
| + | |
| + | Profile Mendelian errors |
| + | |
| + | <div class=" mw-collapsible mw-collapsed"> |
| + | #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 |
| + | |
| + | |
| + | |
| + | <div class="mw-collapsible-content"> |
| + | 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 |
| + | </div> |
| + | </div> |
| + | |
| | | |
| === Profile SNPs === | | === Profile SNPs === |