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Variant classification

49 bytes added, 10:32, 5 September 2014
Output
This is the annotated output of peek in the vt suite.
#This is a sample output of a peek command which summarizes the variants found in a VCF file. stats: no. of samples : 0 #number of genotype fields in VCF file, this is a site list so it is 0 no. of chromosomes : 25 #no. of chromosomes observed in this file.<br>
========== Micro variants ========== <br>
no. of SNP : 54247827#total number of SNPs 2 alleles : 53487808 (1.99) [35616038/17871770] (-nan) [0#ts/0]tv ratio and the respective counts
3 alleles : 389190 (0.60) [291224/487156] (-nan) [0/0]
4 alleles : 370828 (0.50) [370828/741656] (-nan) [0/0]
>=5 alleles : 1 (0.33) [1/3] (-nan) [0/0] <br>
no. of MNP : 122125
2 alleles : 121849 (1.56) [152383/97816] (-nan) [0/0] 3 alleles : 273 (0.89) [537/601] (-nan) [0/0] 4 alleles : 3 (1.00) [9/9] (-nan) [0/0] <br>
no. of Indel : 6600770
2 alleles : 6285861 (-nan) [0/0] (0.88) [2937096/3348765]#ins/del ratio and the respective counts 3 alleles : 280892 (-nan) [0/0] (8.72) [503977/57807] 4 alleles : 28245 (-nan) [0/0] (131.19) [84094/641] >=5 alleles : 5772 (-nan) [0/0] (3847.00) [23082/6] <br>
no. of SNP/MNP : 1161
3 alleles : 1143 (1.57) [1565/994] (-nan) [0/0] 4 alleles : 15 (1.36) [34/25] (-nan) [0/0] >=5 alleles : 3 (0.67) [8/12] (-nan) [0/0] <br>
no. of SNP/Indel : 115153
2 alleles : 42717 (0.65) [16778/25939] (0.57) [15441/27276] #ts/tv and ins/del ratios
3 alleles : 66401 (0.72) [29681/41397] (0.33) [31458/96168]
4 alleles : 4631 (0.55) [2420/4386] (0.25) [2602/10306]
4 alleles : 85 (0.35) [71/203] (0.28) [31/111]
>=5 alleles : 21 (0.35) [24/68] (0.68) [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]
no. of Reference : 0 <br>
====== Other useful categories ===== <br>
no. of Block Substitutions : 184751#equivalent to categories with allele lengths that are the same.
2 alleles : 182466 (1.60) [236793/148036] (-nan) [0/0]
3 alleles : 2247 (1.28) [4544/3538] (-nan) [0/0]
4 alleles : 34 (1.16) [109/94] (-nan) [0/0]
>=5 alleles : 4 (0.76) [13/17] (-nan) [0/0] <br>
no. of Complex Substitutions : 159298#equivalent to categories not including simple SNPs, Block Substitutions and Simple Indels
2 alleles : 81508 (0.61) [60312/98113] (0.66) [32479/49029]
3 alleles : 71003 (0.69) [35811/51840] (0.34) [34268/100942]
1,102
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