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2,767 bytes added, 13:23, 14 February 2016
Profile Indels
#profile indels found in mills.vcf
vt profile_indels -g indel.reference.txt mills.vcf -r hs37d5.fa -i 20
 
#this is a sample output for indel profiling.
# square brackets contain the ins/del ratio.
# for the FS/NFS field, that is the proportion of coding indels that are frame shifted.
# The numbers in curved bracket are the counts of frame shift and non frame shift indels respectively.
data set
No Indels : 46974 [0.89]
FS/NFS : 0.26 (8/23) <br>
dbsnp
A-B 30704 [0.92]
A&B 16270 [0.83]
B-A 2049488 [1.52]
Precision 34.6%
Sensitivity 0.8% <br>
mills
A-B 43234 [0.88]
A&B 3740 [1.00]
B-A 203278 [0.98]
Precision 8.0%
Sensitivity 1.8% <br>
mills.chip
A-B 46847 [0.89]
A&B 127 [0.90]
B-A 8777 [0.93]
Precision 0.3%
Sensitivity 1.4% <br>
affy.exome.chip
A-B 46911 [0.89]
A&B 63 [0.43]
B-A 33997 [0.47]
Precision 0.1%
Sensitivity 0.2% <br>
 
# 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
1000g TP N_ALLELE==2&&VTYPE==INDEL /net/fantasia/home/atks/ref/vt/grch37/1000G.snps_indels.sites.bcf
mills TP N_ALLELE==2&&VTYPE==INDEL /net/fantasia/home/atks/ref/vt/grch37/mills.208620indels.sites.bcf
dbsnp TP N_ALLELE==2&&VTYPE==INDEL /net/fantasia/home/atks/ref/vt/grch37/dbsnp.13147541variants.sites.bcf
GENCODE_V19 cds_annotation . /net/fantasia/home/atks/ref/vt/grch37/gencode.cds.bed.gz
DUST cplx_annotation . /net/fantasia/home/atks/ref/vt/grch37/mdust.bed.gz
 
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usage : vt profile_indels [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>
 
=== Profile VNTRs ===
 
Profile VNTRs. The reference data sets can be obtained from [[Vt#Resource_Bundle|vt resource bundle]].
 
<div class=" mw-collapsible mw-collapsed">
#profile indels found in mills.vcf
vt profile_vntrs -g vntr.reference.txt vt.vcf -r hs37d5.fa
#this is a sample output for indel profiling.
1,102
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