LGenIC

Generates input files for the LymphGen lymphoma classifier. See https://llmpp.nih.gov/lymphgen/index.php.

Description

Using an input MAF file and a TSV file containing copy-number alterations (optional), generate the input files required for use with the LymphGen classifier. Gene IDs are converted from Hugo names to Entrez IDs, and copy number segments are overlapped with gene regions and chromosome arms to identify genes affected by such events

Usage

If you only have single nucleotide variants and small insertions and deletions:

./generate_input.py --lymphgen_genes resources/lymphgen_genes.txt --maf /path/to/maf/file.maf --entrez_ids resources/hugo2entrez.tsv --sequencing_type exome --outdir /path/to/outdir/

Where --maf contains your variants of interest, and their coordinates relative to the GRCh37 reference genome, --entrez_ids is a tab-delineated file with the columns "Approved symbol" and "NCBI Gene ID(supplied by NCBI)". An example file is provided in the resources folder. This file can be downloaded from https://www.genenames.org/download/custom/.

The --lympgen_genes file contains a list of Entrez IDs (one per line) which will be used to subset the output. The default file (in the resources folder) contains the current list of LympghGen SNVs and CNV features.

If you also have CNV info:

./generate_input.py --lymphgen_genes resources/lymphgen_genes.txt --maf /path/to/maf/file.maf --entrez_ids resources/hugo2entrez.tsv --sequencing_type exome --outdir /path/to/outdir/ --cnvs /path/to/cnvs/file.tsv --genes resources/gene_coordinates.bed6 --arms resources/arm_coordinates.tsv

Where --cnvs file has five columns: Tumor_Sample_Barcode, chromosome, start, end, CN. If providing log2 ratios (log2(absoluteCN) - 1), please specify the --log2 flag.

The --genes file is a BED file specifying the coordinates of genes/exons, while the --arms file contains four columns: chromosome, start, arm. Examples of these files can be found in the resources folder. While the --lymphgen_genes file is optional, it is STRONGLY recommended when you are including CNVs, as I have noticed certain copy number features being dropped if too many CNVs are provided to LymphGen

Output

gene_list: A list of Entrez IDs examined. If exome or genome is specified, this contains all genes

sample_annotation: Specifies sample information, and which samples have CN info, BCL2 and BCL6 translocations. If you have SV info, the translocation status of BCL2 and BCL6 should be specified in this file (0=No event, 1=Translocation)

mutation_flat: Contains all mutations. Note that all non-coding mutations (5'UTR, Intron, 5'Flank, silent) are included and labelled as "Synon", as LymphGen automatically confirms which Synon mutations are within 4kb of the TSS

cnv_arm (optional): Lists which samples have CN events affecting more than 80% of a chromosome or chromosome arm

cnv_flat (optional): Specifies genes overlapping copy number events smaller than 30MB