/
QUICK_START
55 lines (43 loc) · 2.27 KB
/
QUICK_START
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
###############################################################################
ALoFT Annotation of Loss of Function Transcripts
QUICK START DOCUMENTATION
Version 1.0 Gerstein Lab
Released 2013 Molecular Biophysics & Biochemistry
Yale University
Citation:
Contact: Dr. Suganthi Balasubramanian (suganthibala@gmail.com)
Mayur Pawashe (mpawashe@gmail.com)
Jeremy Liu (jeremy.liu@yale.edu)
###############################################################################
1. After installing, ALoFT can be run as follows.
$ cd /path/to/aloft_directory
$ ./aloft --vcf=/path/to/vcf_file --data=/path/to/data/dir/ --output=/path/to/output/dir/
The input VCF file supplied by the --vcf option should have a header line
starting with #CHROM or #CHR. For example:
#CHROM POS ID ALT REF ... (precedes any variant data)
Only the first five columns are necessary to have, but the number of columns in
this header line must match with the number of lines in the VCF file. ALoFT
will replace missing columns with 'dummy' entries and compute as usual.
2. Example Workflow: annotating variants from 1000 Genomes variant calls.
Obtain variant calls and vcf files from 1000 Genomes ftp site.
Download to home directory and uncompress.
$ wget [URL NEEDED]
$ [gunzip FILE]
Run the vcf file through aloft, which is installed in the directory aloft
in the home directory and output this to the default directory aloft_output/
$ cd aloft
$ ./aloft --vcf=../[FILE NAME]
To see the aloft output, enter the output directory.
$ cd aloft_output
$ ls
[FILE NAME].aloft.lof (tab delineated output for lof variants)
[FILE NAME].aloft.splice (tab delineated output for splice variants)
[FILE NAME].aloft.vcf (vcf formatted ouptut for all variants)
Run a second time. This time, store the output files in the directory
1000g_aloft_output in the home directory and specify 100bp for the nonsense
mediated decay detection threshold.
$ cd aloft
$ ./aloft --vcf=../[FILE NAME] --output=../1000g_aloft_output/
--nmd_threshold=100
For more information on command line options and output interpretation,
please visit the README.