-
Notifications
You must be signed in to change notification settings - Fork 2
/
12. Check quality of add read group BAM files
128 lines (123 loc) · 6.15 KB
/
12. Check quality of add read group BAM files
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
#!/bin/bash
#SBATCH -n 8
#SBATCH --job-name=Bamtools_STATSperLane
#SBATCH -t 0-2:0
#SBATCH -A mwilsons
#SBATCH -o slurm.Bamtools_STATSperLane.out
#SBATCH -e slurm.Bamtools_STATSperLane.err
#SBATCH --mail-type=END,FAIL
#SBATCH [email protected]
#--------------------------
#--------------------------
# 1. start timer
#--------------------------
date
#--------------------------
# 2. move to directory and load programs
#--------------------------
cd /scratch/kcolney/cancerCellLines_Haynes/2_data/BAM/
module load bamtools/2.4.0
module load java/latest
#--------------------------
# 3. BAMtools index split BAMs
#--------------------------
bamtools stats -in KH1_S1_L001.sort.markdup.readgrps.bam
bamtools stats -in KH1_S1_L002.sort.markdup.readgrps.bam
bamtools stats -in KH1_S1_L003.sort.markdup.readgrps.bam
bamtools stats -in KH1_S1_L004.sort.markdup.readgrps.bam
bamtools stats -in KH2_S2_L001.sort.markdup.readgrps.bam
bamtools stats -in KH2_S2_L002.sort.markdup.readgrps.bam
bamtools stats -in KH2_S2_L003.sort.markdup.readgrps.bam
bamtools stats -in KH2_S2_L004.sort.markdup.readgrps.bam
bamtools stats -in KH3_S3_L001.sort.markdup.readgrps.bam
bamtools stats -in KH3_S3_L002.sort.markdup.readgrps.bam
bamtools stats -in KH3_S3_L003.sort.markdup.readgrps.bam
bamtools stats -in KH3_S3_L004.sort.markdup.readgrps.bam
bamtools stats -in KH4_S4_L001.sort.markdup.readgrps.bam
bamtools stats -in KH4_S4_L002.sort.markdup.readgrps.bam
bamtools stats -in KH4_S4_L003.sort.markdup.readgrps.bam
bamtools stats -in KH4_S4_L004.sort.markdup.readgrps.bam
bamtools stats -in KH5_S5_L001.sort.markdup.readgrps.bam
bamtools stats -in KH5_S5_L002.sort.markdup.readgrps.bam
bamtools stats -in KH5_S5_L003.sort.markdup.readgrps.bam
bamtools stats -in KH5_S5_L004.sort.markdup.readgrps.bam
bamtools stats -in KH6_S6_L001.sort.markdup.readgrps.bam
bamtools stats -in KH6_S6_L002.sort.markdup.readgrps.bam
bamtools stats -in KH6_S6_L003.sort.markdup.readgrps.bam
bamtools stats -in KH6_S6_L004.sort.markdup.readgrps.bam
bamtools stats -in KH7_S7_L001.sort.markdup.readgrps.bam
bamtools stats -in KH7_S7_L002.sort.markdup.readgrps.bam
bamtools stats -in KH7_S7_L003.sort.markdup.readgrps.bam
bamtools stats -in KH7_S7_L004.sort.markdup.readgrps.bam
bamtools stats -in KH8_S8_L001.sort.markdup.readgrps.bam
bamtools stats -in KH8_S8_L002.sort.markdup.readgrps.bam
bamtools stats -in KH8_S8_L003.sort.markdup.readgrps.bam
bamtools stats -in KH8_S8_L004.sort.markdup.readgrps.bam
bamtools stats -in KH9_S1_L001.sort.markdup.readgrps.bam
bamtools stats -in KH9_S1_L002.sort.markdup.readgrps.bam
bamtools stats -in KH9_S1_L003.sort.markdup.readgrps.bam
bamtools stats -in KH9_S1_L004.sort.markdup.readgrps.bam
bamtools stats -in KH10_S2_L001.sort.markdup.readgrps.bam
bamtools stats -in KH10_S2_L004.sort.markdup.readgrps.bam
bamtools stats -in KH10_S2_L002.sort.markdup.readgrps.bam
bamtools stats -in KH10_S2_L003.sort.markdup.readgrps.bam
bamtools stats -in KH11_S3_L001.sort.markdup.readgrps.bam
bamtools stats -in KH11_S3_L002.sort.markdup.readgrps.bam
bamtools stats -in KH11_S3_L003.sort.markdup.readgrps.bam
bamtools stats -in KH11_S3_L004.sort.markdup.readgrps.bam
bamtools stats -in KH12_S4_L001.sort.markdup.readgrps.bam
bamtools stats -in KH12_S4_L002.sort.markdup.readgrps.bam
bamtools stats -in KH12_S4_L003.sort.markdup.readgrps.bam
bamtools stats -in KH12_S4_L004.sort.markdup.readgrps.bam
bamtools stats -in KH13_S5_L001.sort.markdup.readgrps.bam
bamtools stats -in KH13_S5_L002.sort.markdup.readgrps.bam
bamtools stats -in KH13_S5_L003.sort.markdup.readgrps.bam
bamtools stats -in KH13_S5_L004.sort.markdup.readgrps.bam
bamtools stats -in KH14_S6_L001.sort.markdup.readgrps.bam
bamtools stats -in KH14_S6_L002.sort.markdup.readgrps.bam
bamtools stats -in KH14_S6_L003.sort.markdup.readgrps.bam
bamtools stats -in KH14_S6_L004.sort.markdup.readgrps.bam
bamtools stats -in KH15_S7_L001.sort.markdup.readgrps.bam
bamtools stats -in KH15_S7_L002.sort.markdup.readgrps.bam
bamtools stats -in KH15_S7_L003.sort.markdup.readgrps.bam
bamtools stats -in KH15_S7_L004.sort.markdup.readgrps.bam
bamtools stats -in KH16_S8_L001.sort.markdup.readgrps.bam
bamtools stats -in KH16_S8_L002.sort.markdup.readgrps.bam
bamtools stats -in KH16_S8_L003.sort.markdup.readgrps.bam
bamtools stats -in KH16_S8_L004.sort.markdup.readgrps.bam
bamtools stats -in KH17_S9_L001.sort.markdup.readgrps.bam
bamtools stats -in KH17_S9_L002.sort.markdup.readgrps.bam
bamtools stats -in KH17_S9_L003.sort.markdup.readgrps.bam
bamtools stats -in KH17_S9_L004.sort.markdup.readgrps.bam
bamtools stats -in KH18_S9_L001.sort.markdup.readgrps.bam
bamtools stats -in KH18_S9_L002.sort.markdup.readgrps.bam
bamtools stats -in KH18_S9_L003.sort.markdup.readgrps.bam
bamtools stats -in KH18_S9_L004.sort.markdup.readgrps.bam
bamtools stats -in KH19_S10_L001.sort.markdup.readgrps.bam
bamtools stats -in KH19_S10_L002.sort.markdup.readgrps.bam
bamtools stats -in KH19_S10_L003.sort.markdup.readgrps.bam
bamtools stats -in KH19_S10_L004.sort.markdup.readgrps.bam
bamtools stats -in KH20_S10_L001.sort.markdup.readgrps.bam
bamtools stats -in KH20_S10_L002.sort.markdup.readgrps.bam
bamtools stats -in KH20_S10_L003.sort.markdup.readgrps.bam
bamtools stats -in KH20_S10_L004.sort.markdup.readgrps.bam
bamtools stats -in KH21_S11_L001.sort.markdup.readgrps.bam
bamtools stats -in KH21_S11_L002.sort.markdup.readgrps.bam
bamtools stats -in KH21_S11_L003.sort.markdup.readgrps.bam
bamtools stats -in KH21_S11_L004.sort.markdup.readgrps.bam
bamtools stats -in KH22_S11_L001.sort.markdup.readgrps.bam
bamtools stats -in KH22_S11_L002.sort.markdup.readgrps.bam
bamtools stats -in KH22_S11_L003.sort.markdup.readgrps.bam
bamtools stats -in KH22_S11_L004.sort.markdup.readgrps.bam
bamtools stats -in KH23_S12_L001.sort.markdup.readgrps.bam
bamtools stats -in KH23_S12_L002.sort.markdup.readgrps.bam
bamtools stats -in KH23_S12_L003.sort.markdup.readgrps.bam
bamtools stats -in KH23_S12_L004.sort.markdup.readgrps.bam
bamtools stats -in KH24_S12_L001.sort.markdup.readgrps.bam
bamtools stats -in KH24_S12_L002.sort.markdup.readgrps.bam
bamtools stats -in KH24_S12_L003.sort.markdup.readgrps.bam
bamtools stats -in KH24_S12_L004.sort.markdup.readgrps.bam
#--------------------------
# 4. end timer
#--------------------------
date