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| = Definitions = | | = Definitions = |
| | | |
− | The normalization of a variant representation in VCF consists of two parts: parsimony and left alignment pertaining to the nature of a variant's length and position respectively. | + | The normalization of a variant representation in VCF consists of two parts: parsimony and left alignment pertaining to the nature of a variant's length and position respectively. |
| | | |
| + | == Example == |
| | | |
| + | |
| + | Summarizes the variants in a VCF file |
| + | |
| + | <div class=" mw-collapsible mw-collapsed"> |
| + | #summarizes the variants found in mills.vcf |
| + | vt peek mills.vcf |
| + | |
| + | <div class="mw-collapsible-content"> |
| + | usage : vt peek [options] <in.vcf> |
| + | |
| + | options : -o output VCF file [-] |
| + | -I file containing list of intervals [] |
| + | -i intervals [] |
| + | -r reference sequence fasta file [] |
| + | -- ignores the rest of the labeled arguments following this flag |
| + | -h displays help |
| + | </div> |
| + | </div> |
| + | |
| + | #This is a sample output of a peek command which summarizes the variants found in a VCF file. |
| + | stats: no. of samples : 0 |
| + | no. of chromosomes : 22<br> |
| + | ========== Micro variants ==========<br> |
| + | no. of SNPs : 77228885 |
| + | 2 alleles (ts/tv) : 77011302 (2.11) [52287790/24723512] |
| + | 3 alleles (ts/tv) : 216560 (0.75) [185520/247600] |
| + | 4 alleles (ts/tv) : 1023 (0.50) [1023/2046]<br> |
| + | no. of MNPs : 0 |
| + | 2 alleles (ts/tv) : 0 (-nan) [0/0] |
| + | >=3 alleles (ts/tv) : 0 (-nan) [0/0]<br> |
| + | no. Indels : 2147564 |
| + | 2 alleles (ins/del) : 2124842 (0.47) [683250/1441592] |
| + | >=3 alleles (ins/del) : 22722 (2.12) [32411/15286]<br> |
| + | no. SNP/MNP : 0 |
| + | 3 alleles (ts/tv) : 0 (-nan) [0/0] |
| + | >=4 alleles (ts/tv) : 0 (-nan) [0/0] <br> |
| + | no. SNP/Indels : 12913 |
| + | 2 alleles (ts/tv) (ins/del) : 412 (0.41) [120/292] (3.68) [324/88] |
| + | >=3 alleles (ts/tv) (ins/del) : 12501 (0.43) [7670/17649] (18.64) [12434/667]<br> |
| + | no. MNP/Indels : 153 |
| + | 2 alleles (ts/tv) (ins/del) : 0 (-nan) [0/0] (-nan) [0/0] |
| + | >=3 alleles (ts/tv) (ins/del) : 153 (0.30) [138/465] (0.27) [67/248]<br> |
| + | no. SNP/MNP/Indels : 2 |
| + | 3 alleles (ts/tv) (ins/del) : 0 (-nan) [0/0] (-nan) [0/0] |
| + | 4 alleles (ts/tv) (ins/del) : 2 (0.00) [3/5] (1.00) [3/3] |
| + | >=5 alleles (ts/tv) (ins/del) : 0 (-nan) [0/0] (-nan) [0/0]<br> |
| + | no. of clumped variants : 19025 |
| + | 2 alleles : 0 (-nan) [0/0] (-nan) [0/0] |
| + | 3 alleles : 18508 (0.16) [12152/75366] (0.00) [93/18653] |
| + | 4 alleles : 451 (0.15) [369/2390] (0.33) [201/609] |
| + | >=5 alleles : 66 (0.09) [37/414] (1.19) [107/90]<br> |
| + | ====== Other useful categories =====<br> |
| + | no. complex variants : 32093 |
| + | 2 alleles (ts/tv) (ins/del) : 412 (0.41) [120/292] (3.68) [324/88] |
| + | >=3 alleles (ts/tv) (ins/del) : 31681 (0.21) [20369/96289] (0.64) [12905/20270]<br> |
| + | ======= Structural variants ========<br> |
| + | no. of structural variants : 41217 |
| + | 2 alleles : 38079 |
| + | deletion : 13135 |
| + | insertion : 16451 |
| + | mobile element : 16253 |
| + | ALU : 12513 |
| + | LINE1 : 2911 |
| + | SVA : 829 |
| + | numt : 198 |
| + | duplication : 664 |
| + | inversion : 100 |
| + | copy number variation : 7729 |
| + | >=3 alleles : 3138 |
| + | copy number variation : 3138 <br> |
| + | ========= General summary ========== <br> |
| + | no. of reference : 0 <br> |
| + | no. of observed variants : 79449759 |
| + | no. of unclassified variants : 0 |
| | | |
| = Maintained by = | | = Maintained by = |
| | | |
| This page is maintained by [mailto:atks@umich.edu Adrian]. | | This page is maintained by [mailto:atks@umich.edu Adrian]. |