Difference between revisions of "Vpeep"
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user@host:~$ vpeep CGI.public.69genomes.PASS.nonsnps.vcf | user@host:~$ vpeep CGI.public.69genomes.PASS.nonsnps.vcf | ||
− | + | atks@fantasia:~/data/cg$ vpeep CGI.public.69genomes.PASS.nonsnps.vcf | |
− | + | ##fileformat=VCFv4.1 | |
− | + | ##fileDate=20111105 | |
− | + | ##source=CGA Tools v1.3 listvariants/testvariants | |
− | + | ##reference=/sup/sv-01/users/scordes/cgatools_files/build37.crr | |
− | + | ##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples with Fully Called Data"> | |
− | + | ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency"> | |
− | + | ##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership"> | |
− | + | ##INFO=<ID=RSID,Number=A,Type=String,Description="dbSNP rs ids"> | |
− | + | ##FILTER=<ID=s50,Description="Less than 50% of samples are fully called"> | |
− | + | ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> | |
− | + | Genotype fields present: 69 individuals | |
− | + | ||
− | + | No. of SNPs : 72798 | |
− | + | 2 alleles : 12 | |
− | + | 3 alleles : 72518 | |
− | + | 4 alleles : 268 | |
− | + | No. of MNPs : 490286 | |
− | + | Length 2 : 297135 | |
− | + | Length 3 : 155284 | |
− | + | Length 4 : 21621 | |
− | + | Length >=5 : 16246 | |
− | + | No. of INDELs : 3905430 | |
− | + | Insertions : 1837950 | |
− | + | Deletions : 1931173 | |
− | + | Multiallelic : 136307 | |
− | + | No. of SVs : 2506 | |
− | + | Precise : 2506 | |
− | + | Unprecise : 0 | |
− | + | No. of CRs : 0 | |
− | + | Total No. of Variants : 4471020 | |
− | + | ||
− | + | INDEL GALD - 1 to 50 | |
− | + | SV GALD - 51 to 194 | |
− | + | ||
− | + | SNP - Single Nucleotide Polymorphism | |
− | + | MNP - Multiple Nucleotide Polymorphism | |
− | + | INDEL - Insertions and Deletions (GALD<=50) | |
− | + | SV - Structural Variants (GALD>50) | |
− | + | CR - Chromosomal Rearrangements | |
− | + | ||
− | + | GALD - Greatest Allele Length Difference | |
− | + | defined as greatest length difference amongst all alleles | |
− | + | Precise - SV alternative allele denoted in the same way as INDELs | |
− | + | Unprecise - SV alternative allele denoted by <INS:ME:L1> for example | |
== Access == | == Access == |
Revision as of 11:48, 19 January 2012
vpeep checks the distribution in a VCF file.
Basic Usage Example
vpeep <vcf-file>
example: vpeep pscalare.vcf
Output
user@host:~$ vpeep CGI.public.69genomes.PASS.nonsnps.vcf atks@fantasia:~/data/cg$ vpeep CGI.public.69genomes.PASS.nonsnps.vcf
##fileformat=VCFv4.1 ##fileDate=20111105 ##source=CGA Tools v1.3 listvariants/testvariants ##reference=/sup/sv-01/users/scordes/cgatools_files/build37.crr ##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples with Fully Called Data"> ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency"> ##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership"> ##INFO=<ID=RSID,Number=A,Type=String,Description="dbSNP rs ids"> ##FILTER=<ID=s50,Description="Less than 50% of samples are fully called"> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> Genotype fields present: 69 individuals No. of SNPs : 72798 2 alleles : 12 3 alleles : 72518 4 alleles : 268 No. of MNPs : 490286 Length 2 : 297135 Length 3 : 155284 Length 4 : 21621 Length >=5 : 16246 No. of INDELs : 3905430 Insertions : 1837950 Deletions : 1931173 Multiallelic : 136307 No. of SVs : 2506 Precise : 2506 Unprecise : 0 No. of CRs : 0 Total No. of Variants : 4471020 INDEL GALD - 1 to 50 SV GALD - 51 to 194 SNP - Single Nucleotide Polymorphism MNP - Multiple Nucleotide Polymorphism INDEL - Insertions and Deletions (GALD<=50) SV - Structural Variants (GALD>50) CR - Chromosomal Rearrangements GALD - Greatest Allele Length Difference defined as greatest length difference amongst all alleles Precise - SV alternative allele denoted in the same way as INDELs Unprecise - SV alternative allele denoted by <INS:ME:L1> for example
Access
Point to /net/fantasia/home/atks/programs/vtools for access to tools.
This page is maintained by Adrian.