1,102
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to search→Mac
</div>
</div>
=== Mac ===
You will need to install the package xz prior to installing vt.
homebrew install xz
Building has been tested on Linux and Mac systems on gcc 4.8.1 and clang 3.4. <br>
Some features of C++11 are used, thus there is a need for newer versions of gcc and clang.
= Updating =
= Updating =
<div class=" mw-collapsible mw-collapsed">
<div class=" mw-collapsible mw-collapsed">
#converts in.bcf to tab format with selected INFO fields
#converts in.bcf to tab format with selected INFO and FILTER fields
vt info2tab in.bcf -v -t EX_RL,FZ_RL,MDUST,LOBSTR,VNTRSEEK,RMSK,EX_REPEAT_TRACT
vt info2tab in.bcf -u PASS -t EX_RL,FZ_RL,MDUST,LOBSTR,VNTRSEEK,RMSK,EX_REPEAT_TRACT
<div style="height:6em; overflow:auto; border: 2px solid #FFF">
<div style="height:6em; overflow:auto; border: 2px solid #FFF">
INPUT
=====
20 17548608 . A AC . PASS CENTERS=vbi;NCENTERS=1;OLD_MULTIALLELIC=20:17548598:GAAAAAAAAAAAAA/GAAAAAAAAAAAA/GAAAAAAAAAAAAAA/GAAAAAAAAAA/GAAAAAAAAAAA/GAAAAAAAAAACAAA;OLD_VARIANT=20:17548598:GAAAAAAAAAAAAAG/GAAAAAAAAAACAAAG;EX_MOTIF=C;EX_MLEN=1;EX_RU=C;EX_BASIS=C;EX_BLEN=1;EX_REPEAT_TRACT=17548608,17548609;EX_COMP=100,0,0,0;EX_ENTROPY=0;EX_ENTROPY2=0;EX_KL_DIVERGENCE=2;EX_KL_DIVERGENCE2=4;EX_REF=2;EX_RL=2;EX_LL=3;EX_RU_COUNTS=0,2;EX_SCORE=0;EX_TRF_SCORE=-14;FZ_MOTIF=A;FZ_MLEN=1;FZ_RU=A;FZ_BASIS=A;FZ_BLEN=1;FZ_REPEAT_TRACT=17548599,17548611;FZ_COMP=100,0,0,0;FZ_ENTROPY=0;FZ_ENTROPY2=0;FZ_KL_DIVERGENCE=2;FZ_KL_DIVERGENCE2=4;FZ_REF=13;FZ_RL=13;FZ_LL=14;FZ_RU_COUNTS=13,13;FZ_SCORE=1;FZ_TRF_SCORE=26;FLANKSEQ=GAAAAAAAAA[A]AAAGAAGGAA;MDUST;LOBSTR
20 17548608 . A AC . PASS CENTERS=vbi;NCENTERS=1;OLD_MULTIALLELIC=20:17548598:GAAAAAAAAAAAAA/GAAAAAAAAAAAA/GAAAAAAAAAAAAAA/GAAAAAAAAAA/GAAAAAAAAAAA/GAAAAAAAAAACAAA;OLD_VARIANT=20:17548598:GAAAAAAAAAAAAAG/GAAAAAAAAAACAAAG;EX_MOTIF=C;EX_MLEN=1;EX_RU=C;EX_BASIS=C;EX_BLEN=1;EX_REPEAT_TRACT=17548608,17548609;EX_COMP=100,0,0,0;EX_ENTROPY=0;EX_ENTROPY2=0;EX_KL_DIVERGENCE=2;EX_KL_DIVERGENCE2=4;EX_REF=2;EX_RL=2;EX_LL=3;EX_RU_COUNTS=0,2;EX_SCORE=0;EX_TRF_SCORE=-14;FZ_MOTIF=A;FZ_MLEN=1;FZ_RU=A;FZ_BASIS=A;FZ_BLEN=1;FZ_REPEAT_TRACT=17548599,17548611;FZ_COMP=100,0,0,0;FZ_ENTROPY=0;FZ_ENTROPY2=0;FZ_KL_DIVERGENCE=2;FZ_KL_DIVERGENCE2=4;FZ_REF=13;FZ_RL=13;FZ_LL=14;FZ_RU_COUNTS=13,13;FZ_SCORE=1;FZ_TRF_SCORE=26;FLANKSEQ=GAAAAAAAAA[A]AAAGAAGGAA;MDUST;LOBSTR
20 17548608 . AAAAG A . PASS CENTERS=ox1;NCENTERS=1;EX_MOTIF=AAAG;EX_MLEN=4;EX_RU=AAAG;EX_BASIS=AG;EX_BLEN=2;EX_REPEAT_TRACT=17548609,17548612;EX_COMP=100,0,0,0;EX_ENTROPY=0;EX_ENTROPY2=0;EX_KL_DIVERGENCE=2;EX_KL_DIVERGENCE2=4;EX_REF=0.75;EX_RL=4;EX_LL=4;EX_RU_COUNTS=0,1;EX_SCORE=0.75;EX_TRF_SCORE=-1;FZ_MOTIF=A;FZ_MLEN=1;FZ_RU=A;FZ_BASIS=A;FZ_BLEN=1;FZ_REPEAT_TRACT=17548599,17548611;FZ_COMP=100,0,0,0;FZ_ENTROPY=0;FZ_ENTROPY2=0;FZ_KL_DIVERGENCE=2;FZ_KL_DIVERGENCE2=4;FZ_REF=13;FZ_RL=13;FZ_LL=13;FZ_RU_COUNTS=13,13;FZ_SCORE=1;FZ_TRF_SCORE=26;FLANKSEQ=GAAAAAAAAA[AAAAG]AAGGAACTAC;MDUST;LOBSTR;OLD_VARIANT=20:17548598:GAAAAAAAAAAAAAG/GAAAAAAAAAA
20 17548608 . AAAAG A . PASS CENTERS=ox1;NCENTERS=1;EX_MOTIF=AAAG;EX_MLEN=4;EX_RU=AAAG;EX_BASIS=AG;EX_BLEN=2;EX_REPEAT_TRACT=17548609,17548612;EX_COMP=100,0,0,0;EX_ENTROPY=0;EX_ENTROPY2=0;EX_KL_DIVERGENCE=2;EX_KL_DIVERGENCE2=4;EX_REF=0.75;EX_RL=4;EX_LL=4;EX_RU_COUNTS=0,1;EX_SCORE=0.75;EX_TRF_SCORE=-1;FZ_MOTIF=A;FZ_MLEN=1;FZ_RU=A;FZ_BASIS=A;FZ_BLEN=1;FZ_REPEAT_TRACT=17548599,17548611;FZ_COMP=100,0,0,0;FZ_ENTROPY=0;FZ_ENTROPY2=0;FZ_KL_DIVERGENCE=2;FZ_KL_DIVERGENCE2=4;FZ_REF=13;FZ_RL=13;FZ_LL=13;FZ_RU_COUNTS=13,13;FZ_SCORE=1;FZ_TRF_SCORE=26;FLANKSEQ=GAAAAAAAAA[AAAAG]AAGGAACTAC;MDUST;LOBSTR;OLD_VARIANT=20:17548598:GAAAAAAAAAAAAAG/GAAAAAAAAAA
</div>
</div>
OUTPUT
CHROM POS REF ALT N_ALLELE EX_RL FZ_RL MDUST LOBSTR VNTRSEEK RMSK EX_REPEAT_TRACT_1 EX_REPEAT_TRACT_2
======
20 17548608 A AC 2 2 13 1 1 0 0 17548608 17548608
CHROM POS REF ALT N_ALLELE PASS EX_RL FZ_RL MDUST LOBSTR VNTRSEEK RMSK EX_REPEAT_TRACT_1 EX_REPEAT_TRACT_2
20 17548608 AAAAG A 2 4 13 1 1 0 0 17548609 17548609
20 17548608 A AC 2 1 2 13 1 1 0 0 17548608 17548608
20 17548608 AAAAG A 2 1 4 13 1 1 0 0 17548609 17548609
<div class="mw-collapsible-content">
<div class="mw-collapsible-content">
usage : vt info2tab [options] <in.vcf>
usage : vt info2tab [options] <in.vcf>
options : -v print variant CHROM,POS,REF,ALT,N_ALLELE [false]
options : -d debug [false]
-f filter expression []
-f filter expression []
-t list of info tags to be extracted []
-u list of filter tags to be extracted []-t list of info tags to be extracted []
-o output tab delimited file [-]
-o output tab delimited file [-]
-I file containing list of intervals []
-I file containing list of intervals []
</div>
</div>
=== Profile SNPs ===
=== Profile Mendelian Errors ===
Profile SNPs. The reference data sets can be obtained from [[Vt#Resource_Bundle|vt resource bundle]].
Profile Mendelian errors
<div class=" mw-collapsible mw-collapsed">
<div class=" mw-collapsible mw-collapsed">
#profile snps found in 20.sites.vcf
#profile mendelian errors found in vt.genotypes.bcf, generate [[media:mendel.pdf|tables]] in the directory mendel, requires pdflatex.
vt profile_snps -g snp.reference.txt 20.sites.vcf -r hs37d5.fa -i 20
vt profile_mendelian vt.genotypes.bcf -p trios.ped -x mendel
pedigree file format is described in [[Vt#Pedigree File|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
A&B 398633 [2.37]
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-B 324063 [1.99]
A/A R/A 47 1164 1183 1.96 1.02 49.60
A&B 184540 [2.29]
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. The reference data sets can be obtained from [[Vt#Resource_Bundle|vt resource bundle]].
<div class=" mw-collapsible mw-collapsed">
#profile snps found in 20.sites.vcf
vt profile_snps -g snp.reference.txt 20.sites.vcf -r hs37d5.fa -i 20
#this is a sample output for indel profiling.
# square brackets contain the ts/tv ratio.
# The numbers in curved bracket are the counts of ts and tv SNPs respectively.
# Low complexity shows what percent of the SNPs are in low complexity regions.
data set
No. SNPs : 508603 [2.09]
Low complexity : 0.08 (39837/508603) <br>
1000g
A-B 109970 [1.39]
A&B 398633 [2.37]
B-A 1340682 [2.26]
Precision 78.4%
Sensitivity 22.9% <br>
dbsnp
A-B 324063 [1.99]
A&B 184540 [2.29]
B-A 103893 [2.60]
Precision 36.3%
Sensitivity 64.0%
# 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)
#this is a sample output for indel profiling.
# overlap percentages labeled as (Precision, Sensitivity) and (False Discovery Rate, Type I Error) respectively
# square brackets contain the ins/del ratio.
# - annotation
# for the FS/NFS field, that is the proportion of coding indels that are frame shifted.
# file is used for GENCODE annotation of frame shift and non frame shift Indels
# The numbers in curved bracket are the counts of frame shift and non frame shift indels respectively.
# filter - filter applied to variants for this particular data set
data set
# path - path of indexed BCF file
#dataset type filter path
1000g TP N_ALLELE==2&&VTYPE==SNP /net/fantasia/home/atks/ref/vt/grch37/1000G.v5.snps.indels.complex.svs.sites.bcf
dbsnp TP N_ALLELE==2&&VTYPE==SNP /net/fantasia/home/atks/ref/vt/grch37/dbSNP138.snps.indels.complex.sites.bcf
GENCODE_V19 cds_annotation . /net/fantasia/home/atks/ref/vt/grch37/gencode.v19.cds.bed.gz
DUST cplx_annotation . /net/fantasia/home/atks/ref/vt/grch37/mdust.bed.gz
<div class="mw-collapsible-content">
usage : vt profile_snps [options] <in.vcf>
options : -f filter expression []
-g file containing list of reference datasets []
-I file containing list of intervals []
-i intervals []
-r reference sequence fasta file []
-? displays help
-I file containing list of intervals []
-i intervals []
-r reference sequence fasta file []
-? displays help
</div>
</div>
</div>
</div>
=== Profile VNTRs ===
=== Profile Indels ===
Profile VNTRs. The reference data sets can be obtained from [[Vt#Resource_Bundle|vt resource bundle]].
Profile Indels. The reference data sets can be obtained from [[Vt#Resource_Bundle|vt resource bundle]].
<div class=" mw-collapsible mw-collapsed">
<div class=" mw-collapsible mw-collapsed">
#profile indels found in mills.vcf
vt profile_indels -g indel.reference.txt mills.vcf -r hs37d5.fa -i 20
#profiles a set of VNTRs
#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]
A-B 3269285 #TRs specific to vntrs.sites.bcf
Precision 34.6%
A-B~ 1666185 #TRs in vntrs.sites.bcf that overlap partially with at least one TR in TRF(lobSTR) but does not overlap exactly with another TR.
Sensitivity 0.8% <br>
A&B1 725404 #TRs in vntrs.sites.bcf that overlap exactly with at least one TR in TRF(lobSTR)
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 3291652
A&B 127 [0.90]
A-B~ 1650190
B-A 8777 [0.93]
A&B1 719032
Precision 0.3%
Sensitivity 1.4% <br>
affy.exome.chip
A-B 46911 [0.89]
A&B 63 [0.43]
A-B 5384453
B-A 33997 [0.47]
A-B~ 271302
Precision 0.1%
A&B1 5119
Sensitivity 0.2% <br>
A-B 5660794
A-B~ 79
A&B1 1
# This file contains information on how to process reference data sets.
# This file contains information on how to process reference data sets.
# overlap percentages labeled as (Precision, Sensitivity) and (False Discovery Rate, Type I Error) respectively.
# overlap percentages labeled as (Precision, Sensitivity) and (False Discovery Rate, Type I Error) respectively.
# - annotation.
# - annotation.
# file is used for GENCODE annotation of coding VNTRs.
# file is used for GENCODE annotation of frame shift and non frame shift Indels.
# filter - filter applied to variants for this particular data set.
# filter - filter applied to variants for this particular data set.
# path - path of indexed BCF file.
# path - path of indexed BCF file.
#dataset type filter path
#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
<div class="mw-collapsible-content">
<div class="mw-collapsible-content">
usage : vt profile_vntrs [options] <in.vcf>
usage : vt profile_indels [options] <in.vcf>
options : -g file containing list of reference datasets []
options : -g file containing list of reference datasets []
</div>
</div>
=== Profile Mendelian Errors ===
=== Profile VNTRs ===
Profile Mendelian errors
Profile VNTRs. The reference data sets can be obtained from [[Vt#Resource_Bundle|vt resource bundle]].
<div class=" mw-collapsible mw-collapsed">
<div class=" mw-collapsible mw-collapsed">
#profiles a set of VNTRs
vt profile_vntrs vntrs.sites.bcf -g vntr.reference.txt
profile_vntrs v0.5
no VNTRs 5660874 #number of VNTRs in vntrs.sites.bcf
no low complexity 2686460 (47.46%) #number of VNTRs in low complexity region determined by MDUST
no coding 17911 (0.32%) #number of VNTRs in coding regions determined by GENCODE v7
no redundant 1312209 (23.18%) #number of VNTRs involved in overlapping with one another<br>
trf_lobstr (1638516) #TRF based reference set used in lobSTR, motif lengths 1 to 6.
A-B 3269285 #TRs specific to vntrs.sites.bcf
A-B~ 1666185 #TRs in vntrs.sites.bcf that overlap partially with at least one TR in TRF(lobSTR) but does not overlap exactly with another TR.
A&B1 725404 #TRs in vntrs.sites.bcf that overlap exactly with at least one TR in TRF(lobSTR)
A&B2 723195 #TRs in TRF(lobSTR) that overlap exactly with at least one TR in vntrs.sites.bcf
B-A~ 710075 #TRs in TRF(lobSTR) that overlap partially with at least one TR in vntrs.sites.bcf but does not overlap exactly with another TR.
B-A 205246 #TRs specific to TRF(lobSTR)
#note that the first 3 rows should sum up to the number of TRs in vntrs.sites.bcf
#and the 4th to 6th rows should sum up to the number of TRs in TRF( lobSTR)
#This basically allows us to see the m to n overlapping in overlapping TRs<br>
trf_repeatseq (1624553) #TRF based reference set used in repeatseq, motif lengths 1 to 6.
A-B 3291652
A-B~ 1650190
A&B1 719032
A&B2 716838
B-A~ 703948
B-A 203767 <br>
trf_vntrseek (230306) #TRF based reference set used in vntrseek, motif lengths 7 to 2000.
A-B 5384453
A-B~ 271302
A&B1 5119
A&B2 4973
B-A~ 92496
B-A 132837 <br>
codis+ (15) #CODIS STRs + 2 STRs from PROMEGA
A-B 5660794
A-B~ 79
A&B1 1
A&B2 1
B-A~ 14
B-A 0
# 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 coding VNTRs.
# filter - filter applied to variants for this particular data set.
# path - path of indexed BCF file.
#dataset type filter path
trf_lobstr TP VTYPE==VNTR /net/fantasia/home/atks/ref/vt/grch37/trf.lobstr.sites.bcf
trf_repeatseq TP VTYPE==VNTR /net/fantasia/home/atks/ref/vt/grch37/trf.repeatseq.sites.bcf
trf_vntrseek TP VTYPE==VNTR /net/fantasia/home/atks/ref/vt/grch37/trf.vntrseek.sites.bcf
codis+ TP VTYPE==VNTR /net/fantasia/home/atks/ref/vt/grch37/codis.strs.sites.bcf
GENCODE_V19 cds_annotation . /net/fantasia/home/atks/ref/vt/grch37/gencode.v19.cds.bed.gz
DUST cplx_annotation .
<div class="mw-collapsible-content">
<div class="mw-collapsible-content">
usage : vt discover2 [options]
usage : vt profile_vntrs [options] <in.vcf>
options : -b input BAM/CRAM file
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 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.
</div>
#
# 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 []
options : -L file containing list of input VCF files
-I file containing list of intervals []
-I file containing list of intervals []
-i intervals
-i intervals []
-- ignores the rest of the labeled arguments following this flag
-r reference sequence fasta file []
-h displays help
-? displays help
</div>
</div>
</div>
</div>
=== Remove overlap ===
= Variant Calling =
=== Discover ===
Discovers variants from reads in a BAM/CRAM file.
<div class=" mw-collapsible mw-collapsed">
<div class=" mw-collapsible mw-collapsed">
#annotates indels from VCFs with VNTR information.
#discover variants from NA12878.bam and write to stdout
vt annotate_indels in.vcf -r hs37d5.fa -o annotated.sites.vcf
vt discover -b NA12878.bam -s NA12878 -r hs37d5.fa -i 20
<div class="mw-collapsible-content">
usage : vt discover2 [options]
options : -b input BAM/CRAM file
-y soft clipped unique sequences cutoff [0]
-x soft clipped mean quality cutoff [0]
-w insertion desired type II error [0.0]
-c insertion desired type I error [0.0]
-h insertion fractional evidence cutoff [0]
-g insertion count cutoff [1]
-n deletion desired type II error [0.0]
-m deletion desired type I error [0.0]
-v deletion fractional evidence cutoff [0]
-u deletion count cutoff [1]
-k snp desired type II error [0.0]
-j snp desired type I error [0.0]
-f snp fractional evidence cutoff [0]
-e snp evidence count cutoff [1]
-q base quality cutoff for bases [0]
-C likelihood ratio cutoff [0]
-B reference bias [0]
-a read exclude flag [0x0704]
-l ignore overlapping reads [false]
-t MAPQ cutoff for alignments [0]
-p ploidy [2]
-s sample ID
-r reference sequence fasta file []
-o output VCF file [-]
-z ignore MD tags [0]
-d debug [0]
-I file containing list of intervals []
-i intervals []
-? displays help
</div>
</div>
</div>
=== Merge candidate variants ===
Merge candidate variants across samples. Each VCF file is required to have the FORMAT flags E and N and should have exactly one sample.
<div class=" mw-collapsible mw-collapsed">
#merge candidate variants from VCFs in candidate.txt and output in candidate.sites.vcf
vt merge_candidate_variants candidates.txt -o candidate.sites.vcf
<div class="mw-collapsible-content">
usage : vt merge_candidate_variants [options]
options : -L file containing list of input VCF files
-o output VCF file [-]
-I file containing list of intervals []
-i intervals
-- ignores the rest of the labeled arguments following this flag
-h displays help
</div>
</div>
=== Remove overlap ===
Removes overlapping variants in a VCF file by tagging such variants with the FILTER flag overlap.
<div class=" mw-collapsible mw-collapsed">
#annotates variants that are overlapping
vt remove_overlap in.vcf -r hs37d5.fa -o overlapped.tagged..vcf
<div class="mw-collapsible-content">
usage : vt remove_overlap [options] <in.vcf>
options : -o output VCF file [-]
-I file containing list of intervals []
-i intervals []
-? displays help
</div>
</div>
=== Annotate Indels ===
Annotates indels with VNTR information and adds a VNTR record. Facilitates the simultaneous calling of VNTR together with Indels and SNPs.
<div class=" mw-collapsible mw-collapsed">
#annotates indels from VCFs with VNTR information.
vt annotate_indels in.vcf -r hs37d5.fa -o annotated.sites.vcf
********************************************
<div style="height:20em; overflow:auto; border: 2px solid #FFF">
CHROM POS ID REF ALT QUAL FILTER INFO
20 82079 . G A 1255.98 . NSAMPLES=1;E=43;N=51;ESUM=43;NSUM=51;FLANKSEQ=GGAGCACGCC[G/A]CCATGCCCGG
20 82217 . G A 1632.77 . NSAMPLES=1;E=56;N=61;ESUM=56;NSUM=61;FLANKSEQ=GAGCCACCGC[G/A]CCCGGCCCAG
20 83250 . CTGTGTGTG C . . NSAMPLES=1;E=18;N=35;ESUM=18;NSUM=35;FLANKS=83250,83304;FZ_FLANKS=83250,83303;FLANKSEQ=TCTCTCTCTC[TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT]TTAGTATTTG;GMOTIF=GT;TR=20:83251:TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG:<VNTR>:GT
20 83250 . CTGTGTGTGTG C . . NSAMPLES=1;E=3;N=35;ESUM=3;NSUM=35;FLANKS=83250,83304;FZ_FLANKS=83250,83303;FLANKSEQ=TCTCTCTCTC[TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT]TTAGTATTTG;GMOTIF=GT;TR=20:83251:TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG:<VNTR>:GT
20 83251 . TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG <VNTR> . . MOTIF=GT;RU=TG;FZ_CONCORDANCE=1;FZ_RL=52;FZ_LL=0;FLANKS=83250,83304;FZ_FLANKS=83250,83303;FZ_RU_COUNTS=26,26;FLANKSEQ=TCTCTCTCTC[TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG]TTTAGTATTT
20 83252 . G C 359.204 . NSAMPLES=1;E=13;N=14;ESUM=13;NSUM=14;FLANKSEQ=CTCTCTCTCT[G/C]TGTGTGTGTG
20 83260 . G C 500.163 . NSAMPLES=1;E=18;N=34;ESUM=18;NSUM=34;FLANKSEQ=CTGTGTGTGT[G/C]TGTGTGTGTG
20 83267 . T C 247.043 . NSAMPLES=1;E=11;N=43;ESUM=11;NSUM=43;FLANKSEQ=TGTGTGTGTG[T/C]GTGTGTGTGT
20 83275 . T C 609.669 . NSAMPLES=1;E=24;N=43;ESUM=24;NSUM=43;FLANKSEQ=TGTGTGTGTG[T/C]GTGTGTGTGT
20 90008 . C A 1546.88 . NSAMPLES=1;E=52;N=60;ESUM=52;NSUM=60;FLANKSEQ=AACAGAAAAC[C/A]AAATACTGTA
20 91088 . C T 1766.04 . NSAMPLES=1;E=58;N=66;ESUM=58;NSUM=66;FLANKSEQ=CCCAGCATAC[C/T]ATGGTTGTGC
20 91508 . G A 1266.93 . NSAMPLES=1;E=44;N=53;ESUM=44;NSUM=53;FLANKSEQ=AATTAGTAAG[G/A]CTTACGTAAG
20 91707 . C T 888.134 . NSAMPLES=1;E=30;N=53;ESUM=30;NSUM=53;FLANKSEQ=TGATTTTCTA[C/T]AGCAGGACCT
20 92527 . A G 828.593 . NSAMPLES=1;E=34;N=40;ESUM=34;NSUM=40;FLANKSEQ=ATTAATTGCC[A/G]TTCTCTCTTT
20 93440 . A G 688.144 . NSAMPLES=1;E=24;N=58;ESUM=24;NSUM=58;FLANKSEQ=TTGGATGCAT[A/G]GTCTGTAAAT
20 93636 . TTTTTTCTTTCTTTTTTTTTTTTTTTTTTTTTTTT <VNTR> . . MOTIF=T;RU=T;FZ_CONCORDANCE=0.939394;FZ_RL=35;FZ_LL=0;FLANKS=93646,93671;FZ_FLANKS=93635,93671;FZ_RU_COUNTS=31,33;FLANKSEQ=TCTAGGATTC[TTTTTTCTTTCTTTTTTTTTTTTTTTTTTTTTTTT]GAGATGGAGT
20 93646 . C CT . . NSAMPLES=1;E=2;N=29;ESUM=2;NSUM=29;FLANKS=93646,93671;FZ_FLANKS=93635,93671;FLANKSEQ=TTTTTCTTTC[TTTTTTTTTTTTTTTTTTTTTTTT]GAGATGGAGT;GMOTIF=T;TR=20:93636:TTTTTTCTTTCTTTTTTTTTTTTTTTTTTTTTTTT:<VNTR>:T
20 93717 . A T 31.7622 . NSAMPLES=1;E=2;N=29;ESUM=2;NSUM=29;FLANKSEQ=CAGTGGCGTG[A/T]TCTTAGATCA
20 93931 . G A 628.149 . NSAMPLES=1;E=22;N=53;ESUM=22;NSUM=53;FLANKSEQ=GATTACAGGT[G/A]TGAGCCGCTG
20 100699 . C T 809.09 . NSAMPLES=1;E=28;N=61;ESUM=28;NSUM=61;FLANKSEQ=GGTGAAAAAT[C/T]ACCTGTCAGT
20 101362 . G A 1087.13 . NSAMPLES=1;E=36;N=67;ESUM=36;NSUM=67;FLANKSEQ=TAATACTGAA[G/A]TTTACTTCTC
</div>
The following shows the trace of how the algorithm works
============================================
ANNOTATING INDEL FUZZILY
********************************************
EXTRACTIING REGION BY EXACT LEFT AND RIGHT ALIGNMENT
20:131948:C/CCA
EXACT REGION 131948-131965 (18)
CCACACACACACACACAA
FINAL EXACT REGION 131948-131965 (18)
CCACACACACACACACAA
********************************************
PICK CANDIDATE MOTIFS
Longest Allele : C[CA]CACACACACACACACAA
detecting motifs for an str
seq: CCACACACACACACACACAA
len : 20
cmax_len : 10
candidate motifs: 25
AC : 0.894737 2 0
AAC : 0.5 3 0.0555556
ACC : 0.5 3 0.0555556
AAAC : 0.0588235 4 0.125 (< 2 copies)
ACCC : 0.0588235 4 0.125 (< 2 copies)
AACAC : 0.5 5 0.02
ACACC : 0.5 5 0.02
AAACAC : 0.0666667 6 0.0555556 (< 2 copies)
ACACCC : 0.0666667 6 0.0555556 (< 2 copies)
AACACAC : 0.5 7 0.0102041
ACACACC : 0.5 7 0.0102041
AAACACAC : 0.0769231 8 0.03125 (< 2 copies)
ACACACCC : 0.0769231 8 0.03125 (< 2 copies)
AACACACAC : 0.5 9 0.00617284 (< 2 copies)
ACACACACC : 0.5 9 0.00617284 (< 2 copies)
AAACACACAC : 0.0909091 10 0.02 (< 2 copies)
ACACACACCC : 0.0909091 10 0.02 (< 2 copies)
********************************************
PICKING NEXT BEST MOTIF
selected: AC 0.89 0.00
********************************************
DETECTING REPEAT TRACT FUZZILY
++++++++++++++++++++++++++++++++++++++++++++
++++++++++++++++++++++++++++++++++++++++++++
Exact left/right alignment
repeat_tract : CACACACACACACACA
repeat motif : CA
position : [131949,131964]
motif_concordance : 1
repeat units : 8
exact repeat units : 8
total no. of repeat units : 8
++++++++++++++++++++++++++++++++++++++++++++
Fuzzy right alignment
repeat motif : CA
rflank : AACTC
mlen : 2
mlen : 2
rflen : 5
plen : 111
plen : 111
read : ATCTTACACCACACACACACACACAAACTCAAAATGGATTTAAAGACTTAAATGTGAGCCTGGCAAACTTAAAACTCCTAAAATAAAACAGAAGGGAATATCTTT
read : AGAAATGATAGTCACTTCAACAGATGGTGTTGGGAAAACTGGATTTCCACAGGCAGAACAAATGAAATGGATCCTTATCTTACACCACACACACACACACAAACTC
rlen : 105
rlen : 106
optimal score: 50.5858
optimal score: 50.5073
optimal state: Z
optimal state: MR
optimal track: Z|m|10|2
optimal track: MR|r|0|5
optimal probe len: 26
optimal probe len: 25
optimal path length : 106
optimal path length : 107
max j: 105
max j: 106
probe: (1~82) [1~10] (1~5)
read : (1~82) [83~101] (102~106)
motif # : 10 [83,101]
motif # : 10 [7,25]
motif concordance : 95% (9/10)
motif concordance : 95% (9/10)
motif discordance : 0|1|0|0|0|0|0|0|0|0
motif discordance : 0|1|0|0|0|0|0|0|0|0
Model: ATCTTACACACACACACACACACACA--------------------------------------------------------------------------------
Model: ----------------------------------------------------------------------------------CACACACACACACACACACAAACTC
SYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYMMMDMMMMMMMMMMMMMMMMMMMMME
oo++oo++oo++oo++oo++RRRRR
Read: ATCTTACAC-CACACACACACACACAAACTCAAAATGGATTTAAAGACTTAAATGTGAGCCTGGCAAACTTAAAACTCCTAAAATAAAACAGAAGGGAATATCTTT
Read: AGAAATGATAGTCACTTCAACAGATGGTGTTGGGAAAACTGGATTTCCACAGGCAGAACAAATGAAATGGATCCTTATCTTACAC-CACACACACACACACAAACTC
++++++++++++++++++++++++++++++++++++++++++++
Fuzzy left alignment
lflank : ATCTTA
repeat motif : CA
lflen : 6
mlen : 2
plen : 111
read : ATCTTACACCACACACACACACACAAACTCAAAATGGATTTAAAGACTTAAATGTGAGCCTGGCAAACTTAAAACTCCTAAAATAAAACAGAAGGGAATATCTTT
rlen : 105
Fuzzy
optimal score: 50.5858
repeat_tract : CACCACACACACACACACA
optimal state: Z
position : [131946,131964]
optimal track: Z|m|10|2
reference repeat unit length : 19
optimal probe len: 26
motif_concordance : 0.95
optimal path length : 106
repeat units : 19
max j: 105
exact repeat units : 9
mismatch penalty: 3
total no. of repeat units : 10
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
model: (1~6) [1~10]
read : (1~6) [7~25][26~106]
<div class="mw-collapsible-content">
usage : vt annotate_indels [options] <in.vcf>
motif # : 10 [7,25]
motif concordance : 95% (9/10)
options : -v add vntr record [false]
motif discordance : 0|1|0|0|0|0|0|0|0|0
-x override tags [false]
-f filter expression []
Model: ATCTTACACACACACACACACACACA--------------------------------------------------------------------------------
-d debug [false]
SMMMMMMMMMDMMMMMMMMMMMMMMMMZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZE
-m mode [f]
LLLLLLoo++oo++oo++oo++oo++
e : by exact alignment f : by fuzzy alignment
Read: ATCTTACAC-CACACACACACACACAAACTCAAAATGGATTTAAAGACTTAAATGTGAGCCTGGCAAACTTAAAACTCCTAAAATAAAACAGAAGGGAATATCTTT
-c classification schemas of tandem repeat [6]
1 : lai2003
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
2 : kelkar2008
VNTR Summary
3 : fondon2012
rid : 19
4 : ananda2013
motif : AC
5 : willems2014
ru : CA
6 : tan_kang2015
-a annotation type [v]
Exact
v : a. output VNTR variant (defined by classification).
repeat_tract : CACACACACACACACA
RU repeat unit on reference sequence (CA)
position : [131949,131964]
MOTIF canonical representation (AC)
reference repeat unit length : 8
RL repeat tract length in bases (11)
motif_concordance : 1
FLANKS flanking positions of repeat tract determined by exact alignment
repeat units : 8
RU_COUNTS number of exact repeat units and total number of repeat units in
exact repeat units : 8
repeat tract determined by exact alignment
total no. of repeat units : 8
FZ_RL fuzzy repeat tract length in bases (11)
FZ_FLANKS flanking positions of repeat tract determined by fuzzy alignment
Fuzzy
FZ_RU_COUNTS number of exact repeat units and total number of repeat units in
repeat_tract : CACCACACACACACACACA
repeat tract determined by fuzzy alignment
position : [131946,131964]
FLANKSEQ flanking sequence of indel
reference repeat unit length : 19
LARGE_REPEAT_REGION repeat region exceeding 2000bp
motif_concordance : 0.95
b. mark indels with overlapping VNTR.
repeat units : 19
FLANKS flanking positions of repeat tract determined by exact alignment
exact repeat units : 9
FZ_FLANKS flanking positions of repeat tract determined by fuzzy alignment
total no. of repeat units : 10
GMOTIF generating motif used in fuzzy alignment
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
TR position and alleles of VNTR (20:23413:CACACACACAC:<VNTR>)
a : annotate each indel with RU, RL, MOTIF, REF.
<div class="mw-collapsible-content">
-r reference sequence fasta file []
usage : vt annotate_indels [options] <in.vcf>
-o output VCF file [-]
-I file containing list of intervals []
options : -v add vntr record [false]
-i intervals
-x override tags [false]
-? displays help
-f filter expression []
</div>
-d debug [false]
</div>
-m mode [f]
e : by exact alignment f : by fuzzy alignment
=== Construct Probes ===
-c classification schemas of tandem repeat [6]
1 : lai2003
2 : kelkar2008
3 : fondon2012
4 : ananda2013
5 : willems2014
6 : tan_kang2015
-a annotation type [v]
v : a. output VNTR variant (defined by classification).
RU repeat unit on reference sequence (CA)
MOTIF canonical representation (AC)
RL repeat tract length in bases (11)
FLANKS flanking positions of repeat tract determined by exact alignment
RU_COUNTS number of exact repeat units and total number of repeat units in
repeat tract determined by exact alignment
FZ_RL fuzzy repeat tract length in bases (11)
FZ_FLANKS flanking positions of repeat tract determined by fuzzy alignment
FZ_RU_COUNTS number of exact repeat units and total number of repeat units in
repeat tract determined by fuzzy alignment
FLANKSEQ flanking sequence of indel
LARGE_REPEAT_REGION repeat region exceeding 2000bp
b. mark indels with overlapping VNTR.
FLANKS flanking positions of repeat tract determined by exact alignment
FZ_FLANKS flanking positions of repeat tract determined by fuzzy alignment
GMOTIF generating motif used in fuzzy alignment
TR position and alleles of VNTR (20:23413:CACACACACAC:<VNTR>)
a : annotate each indel with RU, RL, MOTIF, REF.
-r reference sequence fasta file []
-o output VCF file [-]
-I file containing list of intervals []
-i intervals
-? displays help
</div>
</div>
=== Construct Probes ===
#construct probes from candidate.sites.bcf and output to standard out
#construct probes from candidate.sites.bcf and output to standard out
vt construct_probes candidates.sites.bcf -r ref.fa
vt construct_probes candidates.sites.bcf -r ref.fa
<div class="mw-collapsible-content">
<div class="mw-collapsible-content">
usage : vt construct_probes [options] <in.vcf>
usage : vt construct_probes [options] <in.vcf>
options : -o output VCF file [-]
-f minimum flank length [20]
-r reference sequence fasta file []
-I file containing list of intervals []
-i intervals []
-- ignores the rest of the labeled arguments following this flag
-h displays help
</div>
</div>
=== Genotype ===
Genotypes variants for each sample.
<div class=" mw-collapsible mw-collapsed">
#genotypes variants found in candidate.sites.vcf from sample.bam
vt genotype -r seq.fa -b sample.bam -i candidates.sites.vcf -o sample.sites.vcf
<div class="mw-collapsible-content">
usage : vt genotype [options]
options : -r reference sequence fasta file []
-s sample ID []
-o output VCF file [-]
-b input BAM file []
-i input candidate VCF file []
-- ignores the rest of the labeled arguments following this flag
-h displays help
</div>
</div>
= Pedigree File =
vt understands an augmented version introduced by [mailto: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
! scope="col"| Missing Values
|-
|Family ID<br>
Individual ID<br>
Paternal ID<br>
Maternal ID<br>
Sex<br>
Phenotype
|ID of this family <br>
ID(s) of this individual (comma separated) <br>
ID of the father <br>
ID of the mother <br>
Sex of the individual<br>
Phenotype
|[A-Za-z0-9_]+<br>
[A-Za-z0-9_]+(,[A-Za-z0-9_]+)* <br>
[A-Za-z0-9_]+ <br>
[A-Za-z0-9_]+<br>
1=male, 2=female, other, male, female<br>
[A-Za-z0-9_]+
| 0 <br>
cannot be missing <br>
0 <br>
0 <br>
other<br>
-9
|}
Examples:
ceu NA12878 NA12891 NA12892 female -9
yri NA19240 NA19239 NA19238 female -9
ceu NA12878 NA12891 NA12892 2 -9
yri NA19240 NA19239 NA19238 2 -9
#allows tools like profile_mendelian to detect duplicates and check for concordance
ceu NA12878,NA12878A NA12891 NA12892 female case
yri NA19240 NA19239 NA19238 female control
#allows tools like profile_mendelian to detect duplicates and check for concordance
ceu NA12412 0 0 female case
yri NA19650 0 0 female control
= Resource Bundle =
= Resource Bundle =
