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no. of trios : 2
no. of trios : 2
no. of variants : 25346
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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</div>
=== Profile NA12878 ===
Profile Mendelian errors
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#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
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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 =
