Difference between revisions of "Vpeep"

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(Created page with 'Category:Software '''vpeep''' checks the distribution in a VCF file. == Basic Usage Example == vpeep <vcf-file> example: vpeep pscalare.vcf == Output == user…')
 
(Output)
 
(3 intermediate revisions by the same user not shown)
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==  Output ==
 
==  Output ==
  
user@host:~$ vpeep CGI.public.69genomes.PASS.nonsnps.vcf  
+
    user@host:~$ vpeep CGI.public.69genomes.PASS.nonsnps.vcf  
##fileformat=VCFv4.1
+
    ##fileformat=VCFv4.1
##fileDate=20111105
+
    ##fileDate=20111105
##source=CGA Tools v1.3 listvariants/testvariants
+
    ##source=CGA Tools v1.3 listvariants/testvariants
##reference=/sup/sv-01/users/scordes/cgatools_files/build37.crr
+
    ##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=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=AF,Number=A,Type=Float,Description="Allele Frequency">
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
+
    ##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
##INFO=<ID=RSID,Number=A,Type=String,Description="dbSNP rs ids">
+
    ##INFO=<ID=RSID,Number=A,Type=String,Description="dbSNP rs ids">
##FILTER=<ID=s50,Description="Less than 50% of samples are fully called">
+
    ##FILTER=<ID=s50,Description="Less than 50% of samples are fully called">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+
    ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
Genotype fields present: 69 individuals
+
    Genotype fields present: 69 individuals
+
   
No. of SNPs          :      72798
+
    No. of SNPs          :      72798
  2 alleles          :                    12
+
      2 alleles          :                    12
  3 alleles          :                72518
+
      3 alleles          :                72518
  4 alleles          :                  268
+
      4 alleles          :                  268
No. of MNPs          :    490286
+
    No. of MNPs          :    490286
  Length 2            :                297135
+
      Length 2            :                297135
  Length 3            :                155284
+
      Length 3            :                155284
  Length 4            :                21621
+
      Length 4            :                21621
  Length >=5          :                16246
+
      Length >=5          :                16246
No. of INDELs        :    3905430
+
    No. of INDELs        :    3905430
  Insertions          :              1837950
+
      Insertions          :              1837950
  Deletions          :              1931173
+
      Deletions          :              1931173
  Multiallelic        :                136307
+
      Multiallelic        :                136307
No. of SVs            :      2506
+
    No. of SVs            :      2506
  Precise            :                  2506
+
      Precise            :                  2506
  Unprecise          :                    0
+
      Unprecise          :                    0
No. of CRs            :          0
+
    No. of CRs            :          0
Total No. of Variants :    4471020
+
    Total No. of Variants :    4471020
+
   
INDEL GALD - 1 to 50
+
    INDEL GALD - 1 to 50
SV GALD - 51 to 194
+
    SV GALD - 51 to 194
+
   
SNP      - Single Nucleotide Polymorphism
+
    SNP      - Single Nucleotide Polymorphism
MNP      - Multiple Nucleotide Polymorphism
+
    MNP      - Multiple Nucleotide Polymorphism
INDEL    - Insertions and Deletions (GALD<=50)
+
    INDEL    - Insertions and Deletions (GALD<=50)
SV        - Structural Variants (GALD>50)
+
    SV        - Structural Variants (GALD>50)
CR        - Chromosomal Rearrangements
+
    CR        - Chromosomal Rearrangements
+
   
GALD      - Greatest Allele Length Difference
+
    GALD      - Greatest Allele Length Difference
            defined as greatest length difference amongst all alleles
+
                defined as greatest length difference amongst all alleles
Precise  - SV alternative allele denoted in the same way as INDELs
+
    Precise  - SV alternative allele denoted in the same way as INDELs
Unprecise - SV alternative allele denoted by <INS:ME:L1> for example
+
    Unprecise - SV alternative allele denoted by <INS:ME:L1> for example
 
 
  
 
== Access ==
 
== Access ==

Latest revision as of 10:48, 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 
   ##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.