ANNNOVAR variants
Pileup Indel
1. Sample data
chr10 57162 D1 G * homo 26 3 6
chr10 62899 I4 AAAA * hete 31 17 33
chr10 85429 I1 A * homo 38 29 32
chr10 87126 I24 TGCATTTACGTGATCTTGGCTCAC * hete 51 10 38
chr10 87668 D3 CTC * hete 52 27 34
chr10 89301 D1 A * hete 37 7 45
chr10 89448 I3 AGG * hete 27 4 31
chr10 93681 I1 G * hete 21 12 111
chr10 94117 I3 CAA * hete 29 29 81
chr10 94848 D3 TTA * hete 54 7 48
chr10 95775 I1 T * hete 44 6 44
chr10 97572 D1 T * hete 44 8 55
chr10 98719 I1 T * hete 48 13 39
chr10 99022 I1 T * homo 52 19 36
chr10 100224 D6 CCCTAA * hete 41 12 31
chr10 100433 D6 ACCCTC * hete 50 2 20
chr10 100799 I1 G * hete 50 4 22
chr10 101382 D1 G * hete 54 12 39
chr10 101729 D3 GTA * hete 51 19 58
chr10 103093 D1 T * homo 57 23 33
chr10 103731 D2 GA * hete 46 6 28
chr10 106207 D9 TTGTTTTTG * hete 46 6 24
chr10 106216 D4 TTTT * homo 49 11 19
chr10 107344 I1 C * hete 54 6 32
chr10 108119 I1 G * hete 31 7 19
chr10 108176 I1 A * hete 46 3 22
chr10 110565 D2 AA * hete 47 4 11
chr10 110582 D2 AG * hete 51 2 13
chr10 110806 D7 TTTTTTT * hete 55 5 14
chr10 110829 I3 GGG * hete 45 2 13
chr10 111125 I1 T * homo 52 11 14
chr10 112581 D2 CC * homo 30 8 8
chr10 113972 D1 G * hete 56 7 40
chr10 114040 I1 A * hete 57 4 33
chr10 114710 D1 C * hete 56 4 28
chr10 117629 I8 CCAGATCC * hete 42 4 27
chr10 123201 D1 C * homo 58 20 22
vtools show format pileup_indel
INFO: Opening project test.proj
Format: pileup_indels
Description: Input format for samtools pileup indel caller. This format imports
chr, pos, ref, alt and genotype.
variant fields:
chr: Chromosome name
pos: Start position of the indel event.
ref: reference allele, '-' for insertion
alt: alternative allele, '-' for deletion
Genotype field:
genotype: type of indel (homozygote or heterozygote)
3. Example
vtools import --format pileup_indel pileup.indel --build hg18
INFO: Opening project test.proj
INFO: Additional genotype fields: genotype
INFO: Importing genotype from pileup.indel (1/1)
DEBUG: Creating table sample
pileup.indel: 30
INFO: 30 new variants from 30 records are imported, with 0 SNVs, 14 insertions, 16 deletions, and 0 complex variants.
vtools show table variant -l -1
INFO: Opening project test.proj
variant_id, bin, chr, pos, ref, alt
1, 585, 10, 57162, G, -
2, 585, 10, 62899, -, AAAA
3, 585, 10, 85429, -, A
4, 585, 10, 87126, -, TGCATTTACGTGATCTTGGCTCAC
5, 585, 10, 87668, CTC, -
6, 585, 10, 89301, A, -
7, 585, 10, 89448, -, AGG
8, 585, 10, 93681, -, G
9, 585, 10, 94117, -, CAA
10, 585, 10, 94848, TTA, -
11, 585, 10, 95775, -, T
12, 585, 10, 97572, T, -
13, 585, 10, 98719, -, T
14, 585, 10, 99022, -, T
15, 585, 10, 100224, CCCTAA, -
16, 585, 10, 100433, ACCCTC, -
17, 585, 10, 100799, -, G
18, 585, 10, 101382, G, -
19, 585, 10, 101729, GTA, -
20, 585, 10, 103093, T, -
21, 585, 10, 103731, GA, -
22, 585, 10, 106207, TTGTTTTTG, -
23, 585, 10, 106216, TTTT, -
24, 585, 10, 107344, -, C
25, 585, 10, 108119, -, G
26, 585, 10, 108176, -, A
27, 585, 10, 110565, AA, -
28, 585, 10, 110582, AG, -
29, 585, 10, 110806, TTTTTTT, -
30, 585, 10, 110829, -, GGG