Line 1,293: |
Line 1,293: |
| no. of trios : 2 | | no. of trios : 2 |
| no. of variants : 25346 | | 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 NA12878 === |
| + | |
| + | Profile Mendelian errors |
| + | |
| + | <div class=" mw-collapsible mw-collapsed"> |
| + | #profile NA12878 overlap with broad knowledgebase and illumina platinum genomes for the file vt.genotypes.bcf for chromosome 20. |
| + | vt profile_na12878 vt.genotypes.bcf -g na12878.reference.txt -r hs37d5.fa -i 20 |
| + | |
| + | #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 |
| + | data set |
| + | No Indels : 27770 [0.94] |
| + | FS/NFS : 0.26 (8/23) <br> |
| + | broad.kb |
| + | A-B 13071 [1.19] |
| + | A&B 14699 [0.76] |
| + | B-A 21546 [0.62] |
| + | Precision 52.9% |
| + | Sensitivity 40.6% <br> |
| + | illumina.platinum |
| + | A-B 17952 [0.88] |
| + | A&B 9818 [1.07] |
| + | B-A 2418 [0.88] |
| + | Precision 35.4% |
| + | Sensitivity 80.2% <br> |
| + | broad.kb |
| + | R/R R/A A/A ./. |
| + | R/R 346 145 3 5473 |
| + | R/A 3 4133 9 758 |
| + | A/A 2 136 2186 956 |
| + | ./. 2 139 86 322 <br> |
| + | Total genotype pairs : 6963 |
| + | Concordance : 95.72% (6665) |
| + | Discordance : 4.28% (298) <br> |
| + | illumina.platinum |
| + | R/R R/A A/A ./. |
| + | R/R 1768 85 2 0 |
| + | R/A 10 4479 14 0 |
| + | A/A 13 180 3028 0 |
| + | ./. 71 98 70 0<br> |
| + | Total genotype pairs : 9579 |
| + | Concordance : 96.83% (9275) |
| + | Discordance : 3.17% (304) |
| + | |
| + | # This file contains information on how to process reference data sets. |
| + | # |
| + | # dataset - name of data set, this label will be printed. |
| + | # type - True Positives (TP) and False Positives (FP) |
| + | # overlap percentages labeled as (Precision, Sensitivity) and (False Discovery Rate, Type I Error) respectively |
| + | # - annotation |
| + | # file is used for GENCODE annotation of frame shift and non frame shift Indels |
| + | # filter - filter applied to variants for this particular data set |
| + | # path - path of indexed BCF file |
| + | #dataset type filter path |
| + | broad.kb TP PASS /net/fantasia/home/atks/dev/vt/bundle/public/grch37/broad.kb.241365variants.genotypes.bcf |
| + | illumina.platinum TP PASS /net/fantasia/home/atks/dev/vt/bundle/public/grch37/NA12878.illumina.platinum.5284448variants.genotypes.bcf |
| + | #gencode.v19 annotation . /net/fantasia/home/atks/dev/vt/bundle/public/grch37/gencode.v19.annotation.gtf.gz |
| + | <div class="mw-collapsible-content"> |
| + | profile_na12878 v0.5 |
| + | |
| + | usage : vt profile_na12878 [options] <in.vcf> |
| + | |
| + | options : -g file containing list of reference datasets [] |
| + | -I file containing list of intervals [] |
| + | -i intervals [] |
| + | -r reference sequence fasta file [] |
| + | -? displays help |
| + | </div> |
| + | </div> |
| + | |
| + | = Pedigree File = |
| + | |
| + | vt understands an augmented version introduced by [hmkang@umich.edu Hyun] of the PED described by [http://zzz.bwh.harvard.edu/plink/data.shtml#ped plink]. |
| + | |
| + | The pedigree file format is as follows with the following mandatory fields: |
| + | |
| + | {| class="wikitable" |
| + | |- |
| + | ! scope="col"| Field |
| + | ! scope="col"| Description |
| + | ! scope="col"| Valid Values |
| + | |- |
| + | |Family ID<br> |
| + | Individual ID<br> |
| + | Paternal ID<br> |
| + | Maternal ID<br> |
| + | Sex<br> |
| + | Phenotype |
| + | |ID of this family <br> |
| + | ID of this individual <br> |
| + | ID of the father <br> |
| + | ID of the mother <br> |
| + | Sex of the individual. <br> |
| + | Phenotype. |
| + | |[A-Za-z_]+<br> |
| + | [A-Za-z_]+ <br> |
| + | [A-Za-z_]+ <br> |
| + | [A-Za-z_]+<br> |
| + | 1 = male, 2 = female and other = alternative<br> |
| + | [A-Za-z_]+ |
| + | |} |
| + | |
| + | Family ID |
| + | Individual ID |
| + | Paternal ID |
| + | Maternal ID |
| + | Sex (1=male; 2=female; other=unknown) |
| + | Phenotype |
| + | |
| + | |
| + | |
| + | ceu NA12878 NA12891 NA12892 female |
| + | yri NA19240 NA19239 NA19238 female |
| + | |
| + | |
| + | ceu NA12878,NA12878A NA12891 NA12892 female |
| + | yri NA19240 NA19239 NA19238 female |
| + | |
| + | ceu NA12878,NA12878A NA12891 NA12892 0 |
| + | yri NA19240 NA19239 NA19238 0 |
| | | |
| = Variant Calling = | | = Variant Calling = |