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 
   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.