wisekh6 / AmpliconClassifier

AmpliconClassifier

Classify AmpliconArchitect amplicons to determine what type of focal amplification is present.

Current version: 0.2.5

1. Prerequisites:

• Supports both python2 and python3.
• intervaltree (python library): pip install intervaltree
• $AA_DATA_REPO environment variable. For instructions see AmpliconArchitect installation.
• matplotlib (python library, optional): pip install matplotlib

2. Usage:

To generate classifications for a list of amplicons, I recommend doing

python amplicon_classifier.py --ref [hg19, GRCh37, or GRCh38] --input [file with list of your amplicons] > classifier_stdout.log

the --input argument must be formatted as follows, with one amplicon per line:

sample_name_amplicon1 /path/to/sample_name_amplicon1_cycles.txt /path/to/sample_name_amplicon1_graph.txt

Alternatively, you can just classify one amplicon at a time

python amplicon_classifier.py --ref [hg19, GRCh37, or GRCh38] --cycles [/path/to/amplicon_cycles.txt] --graph [/path/to/amplicon_graph.txt] > classifier_stdout.log

There is also an experimental option you can set to visualize the strength of each amplicon class assigned to an amplicon, which can be turned on by setting --plotStyle individual.

If you have data from both GRCh37 and hg19 that you are combining, you can set the flag --add_chr_tag to add the "chr" prefix to each chromosome name and effectively unify everything as hg19-based.

3. Output:

The most important file will be the file [output_prefix]_amplicon_classification_profiles.tsv. This contains an abstract classification of the amplicon, and also indicates in separate columns "BFB+" and "ecDNA+" status.

4. Command line arguments:

Running on a single AA amplicon:

• -c/--cycles: AA cycles file
• -g/--graph: AA graph file

OR running on multiple amplicons

• -i/--input: Tab-separated file containing one or more amplicons formatted as

sample_name_amplicon1 /path/to/sample_name_amplicon1_cycles.txt /path/to/sample_name_amplicon1_graph.txt

Other arguments

• --ref [hg19, GRCh37 or GRCh38]: (Required) Choose reference genome version used in generating AA output.
• -o: Output filename prefix. Default is prefix of -i or -c.
• --add_chr_tag: If you have a mix of hg19 and GRCh37 amplicons, you can set --ref hg19 and --add_chr_tag to classify them all together.
• --min_cn_flow: Minumum cycle CN flow to consider as an amplification (default=1).
• --min_size: Minimum cycle size (in bp) to consider as valid amplicon (default=5000).
• --force: Disable No amp/Invalid class, if possible. Use only when extremely large CN seeds were used in AA amplicon generation.
• --plotStyle [noplot, individual]: Produce a radar-style plot of classification strenghts. Default noplot.