A command tool to view reads over a loci from bam file, like a lightweigth IGV
Project description
MutView
MutView is a tool to view the reads cover a mutation in bam file, output file is html format. It's so fast and efficient, just like a lightweight IGV(Integrative Genomics Viewer).
Requires
- python >= 3.7
- samtools
Installation
pip install mutview
or
pip install git+https://github.com/TuBieJun/MutView.git
Example use
mutview -s -n 250 -c 2 -p 25466919 -r path_of_ref_fasta -S path_of_samtools -b input_bam -o out.html
Argument description
$ mutview
usage: mutview [-h] -p POS -c CHROM -b BAM -r REF -o OUT [-w WINDOW_SIZE] [-s]
[-n NUM_READS] [-q BASE_Q] [-Q ALN_Q] [-f FONT] [-S SAMTOOLS]
optional arguments:
-h, --help show this help message and exit
-p POS, --pos POS the mutation position
-c CHROM, --chrom CHROM
the chrom of mutation
-b BAM, --bam BAM the input bam file
-r REF, --ref REF the reference genome fasta file
-o OUT, --out OUT the output html file
-w WINDOW_SIZE, --window_size WINDOW_SIZE
the window size of reference genome around the
mutation, default is 300
-s, --sort sort as base like igv, default is False
-n NUM_READS, --num_reads NUM_READS
the max reads number to view default is 100
-q BASE_Q, --base_q BASE_Q
the min base quality, reads with bq below the
specified threshold will be lowercases. default is 20.
-Q ALN_Q, --aln_q ALN_Q
the min aln quality, bases with mq below the specified
threshold will be highlighted. default is 20.
-f FONT, --font FONT the the font of the out html file, it should be
monospaced font, default is consolas for windows, if
you view the out html file in mac, you need set the
value to Menlo or other monospaced fonts
-S SAMTOOLS, --samtools SAMTOOLS
the samtools path, default is samtools
Out html Description
- The bases that are inconsistent with the reference genome will be highlighted.
- The bases with quality below the specified threshold will be represented in lowercase letters.
- The background color of reads with alignment quality below the specified threshold will be highlighted.
- Indels are represented using the characters "I" and "_".
- The count of each base type will be displayed at the top
- The left sidebar will display the name of the reads, pair information, and positive/negative strand information.
Here is example out:
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
mutview-0.0.1.tar.gz
(7.0 kB
view hashes)