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(ooO Ooo)
weeSAM { --bam file.bam OR --sam file.sam } --out output.txt
--bam
: The input bam file. [file.bam]
--sam
: The input sam file. [file.sam]
--out
: The name of your output file. [myoutput.txt]
--html
: Generate html for each coverage plot produced by the script. [file.html]
--overwrite
: Add this flag to overwrite a html directory from a previous run.
--mapped
: Add to generate and analyse a new bam file with only mapped reads.
-h
: Print help function.
-v
: weeSAM version number.
Ref_Name
: The identifier of the reference.
Ref_Len
: The length in bases of each reference.
Mapped_Reads
: Number of reads mapped to each reference.
Breadth
: The number of sites in the genome covered by reads.
%_Covered
: The percent of sites in the genome which have coverage.
Min_Depth
: Minimum read depth observed.
Max_Depth
: Max read depth observed.
Avg_Depth
: Mean read depth observed.
Std_Dev
: Standard deviation of the mean (Avg_Depth).
Above_0.2_Depth
: Percentage of sites which have greater than 0.2 * Avg_Depth.
Above_1_Depth
: Percentage of sites which are above Avg_Depth.
Above_1.8_Depth
: Percentage of sites which have greater than 1.8 * Avg_Depth.
Variation_Coefficient
: The mean of Std_Dev of the mean.
You will need pysam
and seaborn
to run weeSAM.
For easy installation of these:
pip install pysam
and
pip install seaborn
Then clone the repo:
git clone https://github.com/centre-for-virus-research/weeSAM.git
Then, weeSAM should work by providing the path to the python script, for example from within repo directory e.g:
./weeSAM -h