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2,029 bytes removed
, 20:43, 15 June 2014
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| First you want to know what is in the bcf file. | | First you want to know what is in the bcf file. |
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− | =Analyses=
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| vt peek all.genotypes.bcf | | vt peek all.genotypes.bcf |
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| options: input VCF file run/final/all.genotypes.bcf | | options: input VCF file run/final/all.genotypes.bcf |
− | [o] output VCF file -
| + | stats: no. of samples : 62 |
− | | + | no. of chromosomes : 1 <br> |
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− | stats: no. of samples : 62 | |
− | no. of chromosomes : 1 | |
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− | no. of SNPs : 0
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− | 2 alleles (ts/tv) : 0 (-nan) [0/0]
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− | 3 alleles (ts/tv) : 0 (-nan) [0/0]
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− | 4 alleles (ts/tv) : 0 (-nan) [0/0]
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− | no. of MNPs : 0
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− | 2 alleles (ts/tv) : 0 (-nan) [0/0]
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− | >=3 alleles (ts/tv) : 0 (-nan) [0/0]
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| no. Indels : 720 | | no. Indels : 720 |
| 2 alleles (ins/del) : 720 (0.84) [328/392] | | 2 alleles (ins/del) : 720 (0.84) [328/392] |
| >=3 alleles (ins/del) : 0 (-nan) [0/0] | | >=3 alleles (ins/del) : 0 (-nan) [0/0] |
− | | + | no. of observed variants : 720 <br> |
− | no. SNP/MNP : 0
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− | 3 alleles (ts/tv) : 0 (-nan) [0/0]
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− | >=4 alleles (ts/tv) : 0 (-nan) [0/0]
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− | no. SNP/Indels : 0
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− | 2 alleles (ts/tv) (ins/del) : 0 (-nan) [0/0] (-nan) [0/0]
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− | >=3 alleles (ts/tv) (ins/del) : 0 (-nan) [0/0] (-nan) [0/0]
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− | no. MNP/Indels : 0
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− | 2 alleles (ts/tv) (ins/del) : 0 (-nan) [0/0] (-nan) [0/0]
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− | >=3 alleles (ts/tv) (ins/del) : 0 (-nan) [0/0] (-nan) [0/0]
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− | no. SNP/MNP/Indels : 0
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− | 3 alleles (ts/tv) (ins/del) : 0 (-nan) [0/0] (-nan) [0/0]
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− | 4 alleles (ts/tv) (ins/del) : 0 (-nan) [0/0] (-nan) [0/0]
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− | >=5 alleles (ts/tv) (ins/del) : 0 (-nan) [0/0] (-nan) [0/0]
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− | no. of clumped variants : 0
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− | 2 alleles : 0 (-nan) [0/0] (-nan) [0/0]
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− | 3 alleles : 0 (-nan) [0/0] (-nan) [0/0]
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− | 4 alleles : 0 (-nan) [0/0] (-nan) [0/0]
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− | >=5 alleles : 0 (-nan) [0/0] (-nan) [0/0]
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− | no. of reference : 0
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− | no. of observed variants : 720 | |
− | no. of unclassified variants : 0
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− | Time elapsed: 0.01s
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| == Comparison with other data sets == | | == Comparison with other data sets == |