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