Vpeep

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 ##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.