Amino Acid Coverage

Builds an amino acid census and returns its coverage.

Basic Usage

quasitools aacoverage [options] <BAM file> <reference file> <bed file>  

Arguments

BAM File

A BAM file (.bam) of sequences aligned to a related reference. A BAM index file (.bai) is also required and should be named the same as the BAM file, with the extension instead changed from ".bam" to ".bai".

Reference File

A reference file related to the aligned BAM sequences. The provided reference file must be the same reference file used when producing the BAM and BAM index files.

BED File

A BED file that specifies the coordinates of genes, with repsect to the provided reference. This BED file must be a BED4+ file. That is, the BED file must contain at least the first 4 BED file columns.

Options

Output

-o, --output FILENAME

The file output location of the amino acid coverage.

Output

The amino acid coverage will be output in CSV format. The output will have one entry per line, with the amino acid position and the coverage at that position. By default, this will be printed to standard output. The user may direct the output to a file by specifying a file name with the -o/--output option.

Applications

• Generating a report of the amino acid coverage, with respect to a referemce, from a BAM alignment file.

Example

Data

The following example data may be used to run the tool:

• hiv.fasta
• hiv.bed
• variant.bam
• variant.bai

Command

quasitools aacoverage variant.bam hiv.fasta hiv.bed

Output

frame: 0
1,0
2,4
3,5
4,9
5,11
6,13
7,15
8,17
9,21
10,22
11,26
12,26
13,28
14,32
15,33
16,37
17,38
18,43
19,44
20,45
21,50
22,54
23,57

(output truncated)