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Variant classification

3,304 bytes added, 10:23, 5 September 2014
Output
#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 : 2225 <br> ========== Micro variants ==========<br> no. of SNPs SNP : 7722888554247827 2 alleles (ts/tv) : 77011302 53487808 (21.1199) [5228779035616038/2472351217871770] (-nan) [0/0] 3 alleles (ts/tv) : 216560 389190 (0.7560) [185520291224/487156] (-nan) [0/2476000] 4 alleles : 370828 (ts0.50) [370828/tv741656] (-nan) [0/0] >=5 alleles : 1023 1 (0.5033) [1/3] (-nan) [10230/20460]<br> no. of MNPs MNP : 0 122125 2 alleles : 121849 (ts1.56) [152383/tv) : 0 97816] (-nan) [0/0] >= 3 alleles : 273 (ts0.89) [537/tv601] (-nan) [0/0] 4 alleles : 0 3 (1.00) [9/9] (-nan) [0/0]<br> no. Indels of Indel : 21475646600770 2 alleles : 6285861 (-nan) [0/0] (0.88) [2937096/3348765] 3 alleles : 280892 (ins-nan) [0/del0] (8.72) [503977/57807] 4 alleles : 2124842 28245 (-nan) [0/0] (131.4719) [68325084094/1441592641] >=3 5 alleles : 5772 (ins-nan) [0/del) : 22722 0] (23847.1200) [3241123082/152866]<br> no. of SNP/MNP : 0 1161 3 alleles : 1143 (ts1.57) [1565/tv) : 0 994] (-nan) [0/0] >= 4 alleles : 15 (ts1.36) [34/tv25] (-nan) [0/0] >=5 alleles : 3 (0 .67) [8/12] (-nan) [0/0] <br> no. of SNP/Indels Indel : 12913 115153 2 alleles : 42717 (ts0.65) [16778/tv25939] (0.57) [15441/27276] 3 alleles : 66401 (ins0.72) [29681/del41397] (0.33) [31458/96168] 4 alleles : 412 4631 (0.4155) [1202420/2924386] (30.6825) [3242602/8810306] >=5 alleles : 1404 (0.62) [1197/1926] (0.10) [513/4989] <br> no. of MNP/Indel : 15619 2 alleles : 12820 (0.51) [12099/23648] (0.77) [5594/7226] 3 alleles : 2455 (ts0.40) [1796/tv4469] (0.45) [1144/2546] 4 alleles : 292 (ins0.24) [215/del891] (1.42) [415/292] >=5 alleles : 12501 52 (0.43) [767096/17649225] (182.6447) [12434126/66751]<br> no. of SNP/MNP/Indels Indel : 153273 2 3 alleles : 167 (ts0.63) [201/tv321] (0.38) [70/184] 4 alleles : 85 (ins0.35) [71/del203] (0.28) [31/111] >=5 alleles : 21 (0 .35) [24/68] (-nan0.68) [25/37]<br> no. of Clumped : 0<br> no. of SNP/Clumped : 0<br> no. of MNP/Clumped : 61175 2 alleles : 60617 (1.68) [84410/50220] (-nan) [0/0] >= 3 alleles : 549 (ts1.23) [1777/tv1449] (-nan) [0/0] 4 alleles : 8 (ins1.43) [53/del37] (-nan) [0/0] >=5 alleles : 153 1 (01.3000) [1385/4655] (0.27-nan) [670/2480]<br> no. of SNP/MNP/Indels Clumped : 2 290 3 alleles : 282 (ts/tv1.35) (ins[665/del) : 0 494] (-nan) [0/0] 4 alleles : 8 (0.57) [13/23] (-nan) [0/0]<br> no. of Indel/Clumped 4 : 27638 2 alleles : 25971 (ts0.65) [31435/tv48526] (0.79) [11444/14527] 3 alleles : 1585 (ins0.74) [3568/del4793] (0.87) [1383/1582] 4 alleles : 2 70 (0.0055) [396/5175] (1.0061) [3124/377] >=5 alleles : 12 (ts0.59) [37/tv63] (4.71) [33/7] <br> no. of SNP/Indel/Clumped : 456 3 alleles : 257 (ins0.84) [332/del394] (0.33) [111/340] 4 alleles : 174 (0 .38) [105/279] (-nan0.58) [186/321] >=5 alleles : 25 (0.19) [12/063] (-nan0.94) [044/047]<br> no. of clumped variants MNP/Indel/Clumped : 19025 153 2 3 alleles : 138 (0 .50) [233/466] (-nan0.84) [102/122] 4 alleles : 12 (0.35) [14/040] (-nan1.42) [017/012] >=5 alleles : 3 alleles : 18508 (0.1664) [121527/7536611] (0.0067) [934/186536]<br> no. of SNP/MNP/Indel/Clumped : 6 4 alleles : 451 1 (03.1500) [3693/23901] (0.3300) [2010/6093] >=5 alleles : 66 5 (0.0962) [378/41413] (12.1900) [10712/906]<br> no. of Reference : 0 <br> ====== Other useful categories =====<br> no. complex variants of Block Substitutions : 32093 184751 2 alleles : 182466 (1.60) [236793/148036] (-nan) [0/0] 3 alleles : 2247 (1.28) [4544/3538] (ts-nan) [0/tv0] 4 alleles : 34 (1.16) [109/94] (-nan) [0/0] >=5 alleles : 4 (ins0.76) [13/del17] (-nan) [0/0] <br> no. of Complex Substitutions : 159298 2 alleles : 412 81508 (0.4161) [12060312/29298113] (30.6866) [32432479/8849029] >= 3 alleles : 71003 (ts0.69) [35811/tv51840] (0.34) [34268/100942] 4 alleles : 5265 (ins0.49) [2924/del5975] (0.30) [3375/11122] >=5 alleles : 31681 1522 (0.2158) [203691381/962892369] (0.6415) [12905757/202705143]<br>
======= Structural variants ========<br>
no. of structural variants : 41217
1,102
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