DIVERS-standalone is intended for users who want to run it locally in a command-line environment (also in GitHub).

Current Version: 1

Programs:

DIVERS-single.py
DIVERS-batch.py

Dependency:

The code is written in python3, and requires bedtools installed.

Datasets:

Download them and put them in the same folder with the DIVERS program.

• DIVERS_Detection_INFO.bed
• DIVERS_Detection_RS.bed
• DIVERS_Detection_RSCRYP.bed

File Format:

Input: Variants in VCF format, with 5 mandatory tab-delimited fields (CHROM, POS, ID, REF, ALT).

Output: DIVERS-detected variants will be output in CSV format, with the following annotations.

• SAMPLE: sample name (only for DIVERS_VCF_batch.py)
• CHROM, POS, ID, REF, ALT: (exactly the same as input)
• STRAND: +/-
• GENE: gene symbol
• TRANSCRIPT: transcript ID (e.g. ENST123456789)
• IVS#: rank of the intron in this gene (e.g., IVS1, IVS2, IVS3)
• RS#: rank of the RS in this intron (e.g., RS1, RS2, RS3)
• RS_CONSEQ: predicted consequences (RS_AGGT_loss, RS_BP_loss, RS_3SS_gain, RS_5SS_gain, RS_CRYP)
• RS_SCORE: weighted confidence score of the RS-site (1-9, the higher the better)
• IVS_SIZE: intron size
• BP_POS: BP position of the RS-site
• PPT_Y: pyrimidine content (%) in the [BP+2, RS-5] region
• RS_START: start position of the essential RS-site
• RS_END: end position of the essential RS-site
• RNASEQ: support from RNA-seq splice junction reads? (Y/N)
• CLIP: support from U2AF eCLIP peaks? (Y/N)
• RNALM: support from RNA language model prediction? (Y/N)
• PHYLOP: all four essential RS-site nucleotides show positive phyloP conservation scores? (Y/N)
• PHASTCONS: RS-site overlaps a conserved element with PhastCons score > 0.5? (Y/N)
• RARE: no human variants with MAF > 0.01% at all four essential RS-site nucleotides? (Y/N)
• All other annotation fields from the input data: Note: if you are using DIVERS_VCF_batch.py, all VCF files should have the same annotation fields.

Command:

    python DIVERS-single.py -i variants.vcf

    arguments:
      -i, --input        input variants in VCF format file
    

    python DIVERS-batch.py -d foldername/ -s samplelist.txt -o output.csv
    
    arguments:
      -d, --dir          directory of VCF files
      -s, --sample       sample list in the above directory (without .vcf extension)
      -o, --output       output filename