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VCFTools on Helix

VCFtools contains a Perl API (Vcf.pm) and a number of Perl scripts that can be used to perform common tasks with VCF files such as file validation, file merging, intersecting, complements, etc. The Perl tools support all versions of the VCF specification (3.2, 3.3, and 4.0), nevertheless, the users are encouraged to use the latest version VCFv4.0. The VCFtools in general have been used mainly with diploid data, but the Perl tools aim to support polyploid data as well.

VCFTools is maintained and developed by Adam Auton, Peter Danecek and collaborators. VCFTools paper.

Programs location

/usr/local/vcftools/bin

Please Note, tabix and bgzip are both under the same directory.

It is important that the environment for VCFtools is set correctly before running the programs. This can be done by typing 'module load vcftools' as in the example below. This only needs to be done once per login session.

How To Use

Example files below can be copied from /usr/local/vcftools/examples/

Example1: Running compare-vcf

helix% module load vcftools helix% cd /data/userID/vcftools/run1 helix% cp /usr/local/vcftools/examples/cmp-test-* . helix% compare-vcf cmp-test-a.vcf.gz cmp-test-b.vcf.gz Number of sites found only in
6 cmp-test-a.vcf.gz (100.0%) cmp-test-b.vcf.gz (100.0%)

Example2: Running vcf-concat


helix% module load vcftools
helix% cd /data/userID/vcftools/run1
helix% cp /usr/local/vcftools/examples/concat-* .
helix% vcf-concat concat-a.vcf.gz concat-b.vcf.gz concat-c.vcf.gz | bgzip -c > out.vcf.gz

Example3: Running vcf-annotate


helix% module load vcftools
helix% cd /data/userID/vcftools/run1
helix% cp /usr/local/vcftools/examples/concat-a.vcf .
helix% cp /usr/local/vcftools/examples/annotate.txt .
helix% bgzip -c annotate.txt > annotate.txt.gz
helix% tabix -p vcf annotate.txt.gz
helix% vcf-annotate -c FROM,TO,CHROM,INFO/HM2,INFO/GN,INFO/DP \
-d key=INFO,ID=HM2,Number=0,Type=Flag,Description="HapMap2 membership" \
-d key=INFO,ID=GN,Number=1,Type=String,Description="Gene Name" \
-d key=INFO,ID=DP,Number=0,Type=Integer,Description="Depth,etc" \
concat-a.vcf -a annotate.txt.gz
##fileformat=VCFv4.0

##INFO=

##FORMAT=

##FORMAT=

##FORMAT=

##FILTER=

##INFO=

##INFO=

##source_20110110.1=/usr/local/vcftools/bin/vcf-annotate -c FROM,TO,CHROM,INFO/HM2,INFO/GN,INFO/DP -d key=INFO,ID=HM2,Number=0,Type=Flag,Description=HapMap2 membership -d key=INFO,ID=GN,Number=1,Type=String,Description=Gene Name -d key=INFO,ID=DP,Number=0,Type=Integer,Description=Depth,etc concat-a.vcf -a annotate.txt.gz

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  A

1       100     .       GTTT    G       1806    q10     DP=5;GN=gene1;HM2       GT:GQ:DP        0/1:409:35

1       110     .       CAAA    C       1792    PASS    DP=6    GT:GQ:DP        0/1:245:32

1       120     .       GA      G       628     q10     DP=21   GT:GQ:DP        1/1:21:21

1       130     .       GAA     G       1016    PASS    DP=7;HM2        GT:GQ:DP        0/1:212:22

1       140     .       GT      G       727     PASS    DP=8    GT:GQ:DP        0/1:150:30

1       150     .       TAAAA   TA,T    246     PASS    DP=9    GT:GQ:DP        1/2:12:10

1       160     .       TAAAA   TA,T    246     PASS    DP=10   GT:GQ:DP        1/2:12:10

2       100     .       GTTT    G       1806    q10     DP=35   GT:GQ:DP        0/1:409:35

2       110     .       CAAA    C       1792    PASS    GN=gene2;HM2    GT:GQ:DP        0/1:245:32

2       120     .       GA      G       628     q10     GN=gene2;HM2    GT:GQ:DP        1/1:21:21

2       130     .       GAA     G       1016    PASS    GN=gene2;HM2    GT:GQ:DP        0/1:212:22

2       140     .       GT      G       727     PASS    GN=gene2;HM2    GT:GQ:DP        0/1:150:30

2       150     .       TAAAA   TA,T    246     PASS    GN=gene2;HM2    GT:GQ:DP        1/2:12:10

2       160     .       TAAAA   TA,T    246     PASS    DP=11;GN=gene3  GT:GQ:DP        1/2:12:10

Documentation

http://vcftools.sourceforge.net/docs.html