# ** CASAVA depth-filtered snp calls **
#$ CMDLINE /CASAVA-1.8.0a19/filterSmallVariants.pl --chrom=chr1
#$ SEQ_MAX_DEPTH chr1 142.345267150165
#
#$ COLUMNS seq_name pos bcalls_used bcalls_filt ref Q(snp) max_gt Q(max_gt) max_gt|poly_site Q(max_gt|poly_site) A_used C_used G_used T_used
chr1 10231 5 9 C 28 AC 28 AC 59 3 2 0 0
chr1 10255 14 29 A 1 AA 9 AT 25 12 0 0 2
chr1 10264 15 19 C 18 AC 18 AC 51 4 11 0 0
chr1 10291 2 16 C 1 CC 10 CT 21 0 1 0 1
chr1 10330 3 14 C 2 CC 5 AC 28 2 1 0 0
chr1 13273 9 0 G 58 CG 54 CG 57 0 6 3 0
chr1 14464 18 0 A 60 AT 60 AT 93 12 0 0 6
chr1 14673 19 0 G 63 CG 63 CG 96 0 8 11 0
chr1 14699 23 0 C 72 CG 72 CG 105 0 14 9 0
chr1 14907 13 0 A 118 AG 65 AG 65 4 0 9 0
chr1 14930 14 2 A 119 AG 68 AG 68 5 0 9 0
chr1 14933 14 2 G 78 AG 78 AG 110 6 0 8 0
chr1 14976 4 0 G 18 AG 18 AG 47 2 0 2 0
chr1 15211 2 0 T 37 GG 5 GG 5 0 0 2 0
chr1 15817 1 0 G 11 GT 3 GT 3 0 0 0 1
chr1 15820 1 0 G 11 GT 3 GT 3 0 0 0 1
chr1 16487 12 0 T 62 CT 62 CT 94 0 6 0 6
chr1 17538 64 0 C 88 AC 88 AC 121 18 46 0 0
chr1 17746 53 1 A 22 AG 22 AG 55 39 0 14 0
chr1 17765 47 1 G 26 AG 26 AG 59 13 0 34 0
chr1 20131 1 0 G 8 CG 2 CG 3 0 1 0 0
chr1 20144 1 0 G 9 AG 2 AG 3 1 0 0 0
chr1 20206 2 0 C 4 CT 4 CT 30 0 1 0 1
chr1 20245 3 0 G 4 AG 4 AG 34 1 0 2 0
chr1 20304 2 0 G 2 GG 5 CG 27 0 1 1 0
vtools import --format Illumina_SNP Illumina_SNP.txt --build hg18
INFO: Opening project f.proj
INFO: Additional genotype fields: Q_max_gt
INFO: Importing genotype from Illumina_SNP.txt (1/1)
Illumina_SNP.txt: 30
The variants are
vtools show table variant -l -1
INFO: Opening project f.proj
variant_id, bin, chr, pos, ref, alt
1, 585, 1, 10231, C, A
2, 585, 1, 10264, C, A
3, 585, 1, 13273, G, C
4, 585, 1, 14464, A, T
5, 585, 1, 14673, G, C
6, 585, 1, 14699, C, G
7, 585, 1, 14907, A, G
8, 585, 1, 14930, A, G
9, 585, 1, 14933, G, A
10, 585, 1, 14976, G, A
11, 585, 1, 15817, G, T
12, 585, 1, 15820, G, T
13, 585, 1, 16487, T, C
14, 585, 1, 17538, C, A
15, 585, 1, 17746, A, G
16, 585, 1, 17765, G, A
17, 585, 1, 20131, G, C
18, 585, 1, 20144, G, A
19, 585, 1, 20206, C, T
20, 585, 1, 20245, G, A