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Revision as of 17:51, 15 June 2014
, 17:51, 15 June 2014→File Preparation
You may also work with vcf.gz, just name the output as *.vcf.gz. But it will be slower with vt.
You may also work with vcf.gz, just name the output as *.vcf.gz. But it will be slower with vt.
=== A quick summary ===
atks@1000g:~/dev/vt/comparisons/seq_workshop$ vt peek run/final/all.genotypes.bcf
peek v0.5
options: input VCF file run/final/all.genotypes.bcf
[o] output VCF file -
stats: no. of samples : 62
no. of chromosomes : 1
no. of SNPs : 0
2 alleles (ts/tv) : 0 (-nan) [0/0]
3 alleles (ts/tv) : 0 (-nan) [0/0]
4 alleles (ts/tv) : 0 (-nan) [0/0]
no. of MNPs : 0
2 alleles (ts/tv) : 0 (-nan) [0/0]
>=3 alleles (ts/tv) : 0 (-nan) [0/0]
no. Indels : 720
2 alleles (ins/del) : 720 (0.84) [328/392]
>=3 alleles (ins/del) : 0 (-nan) [0/0]
no. SNP/MNP : 0
3 alleles (ts/tv) : 0 (-nan) [0/0]
>=4 alleles (ts/tv) : 0 (-nan) [0/0]
no. SNP/Indels : 0
2 alleles (ts/tv) (ins/del) : 0 (-nan) [0/0] (-nan) [0/0]
>=3 alleles (ts/tv) (ins/del) : 0 (-nan) [0/0] (-nan) [0/0]
no. MNP/Indels : 0
2 alleles (ts/tv) (ins/del) : 0 (-nan) [0/0] (-nan) [0/0]
>=3 alleles (ts/tv) (ins/del) : 0 (-nan) [0/0] (-nan) [0/0]
no. SNP/MNP/Indels : 0
3 alleles (ts/tv) (ins/del) : 0 (-nan) [0/0] (-nan) [0/0]
4 alleles (ts/tv) (ins/del) : 0 (-nan) [0/0] (-nan) [0/0]
>=5 alleles (ts/tv) (ins/del) : 0 (-nan) [0/0] (-nan) [0/0]
no. of clumped variants : 0
2 alleles : 0 (-nan) [0/0] (-nan) [0/0]
3 alleles : 0 (-nan) [0/0] (-nan) [0/0]
4 alleles : 0 (-nan) [0/0] (-nan) [0/0]
>=5 alleles : 0 (-nan) [0/0] (-nan) [0/0]
no. of reference : 0
no. of observed variants : 720
no. of unclassified variants : 0
Time elapsed: 0.01s
==Peek==
==Peek==
