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[[Category:Software]]
'''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 [mailto:atks@umich.edu Adrian].
'''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 [mailto:atks@umich.edu Adrian].
