Sortie 13 : exemple de sortie vt peek - Dioufamad/SNPs_Calling GitHub Wiki
khamasiga@N55SL:~/Downloads$ vt peek cosmic-v68-GRCh37.vcf.gz peek v0.5
options: input VCF file cosmic-v68-GRCh37.vcf.gz
stats: no. of samples : 0 no. of chromosomes : 25
========== Micro variants ==========
no. of SNP : 1088819
2 alleles : 1067646 (1.38) [619708/447938]
3 alleles : 20361 (0.78) [17783/22939]
4 alleles : 810 (0.50) [809/1621]
>=5 alleles : 2 (0.33) [2/6]
no. of MNP : 6421
2 alleles : 6371 (0.89) [6019/6794]
3 alleles : 40 (0.69) [71/103]
4 alleles : 7 (0.72) [18/25]
>=5 alleles : 3 (0.41) [7/17]
no. of INDEL : 43452
2 alleles : 40850 (0.34) [10431/30419]
3 alleles : 2133 (0.75) [1833/2433]
4 alleles : 305 (0.65) [359/556]
>=5 alleles : 164 (0.79) [289/367]
no. of SNP/MNP : 87
2 alleles : 85 (0.60) [32/53]
3 alleles : 2 (0.25) [1/4]
no. of SNP/INDEL : 243
2 alleles : 173 (0.43) [52/121] (0.24) [33/140]
3 alleles : 35 (0.84) [16/19] (0.59) [26/44]
4 alleles : 20 (0.17) [3/18] (1.07) [31/29]
>=5 alleles : 15 (0.36) [5/14] (1.31) [34/26]
no. of MNP/INDEL : 117
2 alleles : 81 (0.46) [84/182] (0.31) [19/62]
3 alleles : 19 (0.20) [13/65] (0.65) [15/23]
4 alleles : 8 (0.19) [5/27] (5.00) [20/4]
>=5 alleles : 9 (0.44) [7/16] (0.80) [16/20]
no. of SNP/MNP/INDEL : 13
3 alleles : 4 (0.40) [6/15] (1.00) [4/4]
4 alleles : 3 (0.12) [1/8] (0.00) [0/9]
>=5 alleles : 6 (0.30) [3/10] (1.40) [14/10]
no. of MNP/CLUMPED : 86
2 alleles : 74 (0.68) [127/187]
3 alleles : 6 (0.87) [13/15]
4 alleles : 3 (0.80) [8/10]
>=5 alleles : 3 (0.86) [12/14]
no. of INDEL/CLUMPED : 171
2 alleles : 126 (0.24) [24/102]
3 alleles : 22 (0.38) [12/32]
4 alleles : 7 (0.31) [5/16]
>=5 alleles : 16 (0.94) [31/33]
no. of SNP/INDEL/CLUMPED : 11
4 alleles : 3 (0.43) [3/7] (0.50) [3/6]
>=5 alleles : 8 (0.11) [3/27] (2.20) [22/10]
no. of MNP/INDEL/CLUMPED : 10
3 alleles : 1 (0.50) [1/2] (1.00) [1/1]
4 alleles : 1 (0.33) [2/6] (0.00) [0/3]
>=5 alleles : 8 (0.32) [15/47] (2.20) [22/10]
no. of SNP/MNP/INDEL/CLUMPED : 13
4 alleles : 1 (0.38) [3/8] (inf) [3/0]
>=5 alleles : 12 (0.47) [36/76] (0.50) [16/32]
no. of micro variants : 1139443
++++++ Other useful categories +++++
no. of clumped variants : 291
2 alleles : 200 (0.55) [365/660] (0.24) [24/102]
3 alleles : 29 (0.54) [93/171] (0.39) [13/33]
4 alleles : 15 (0.55) [24/44] (0.44) [11/25]
>=5 alleles : 47 (0.43) [87/204] (1.07) [91/85]
no. of block substitutions : 6594
2 alleles : 6530 (0.88) [6178/7034]
3 alleles : 48 (0.70) [85/122]
4 alleles : 10 (0.74) [26/35]
>=5 alleles : 6 (0.61) [19/31]
no. of complex substitutions : 578
2 alleles : 380 (0.48) [374/776] (0.25) [76/304]
3 alleles : 81 (0.45) [115/255] (0.56) [58/104]
4 alleles : 43 (0.29) [25/87] (0.93) [62/67]
>=5 alleles : 74 (0.39) [90/230] (1.10) [155/141]
========= General summary ==========
no. of VCF records : 1139485
no. of reference records : 42
no. of classified variants : 1139443
Time elapsed: 1.38s
khamasiga@N55SL:~/Downloads$