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_VCF_one.py
DIVERS_VCF_batch.py

Dependency:

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

Dataset:

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

DIVERS_Detection.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: the strand +/- where the variant found affecting RS

GENE: gene symbol

TRANSCRIPT: transcript ID (e.g. ENST123456789)

IVS#: the ranking number of the intron in the gene (e.g. IVS1, IVS2, IVS3)

IVS_SIZE: the size of the intron

RS#: the ranking number of the RS in this intron (e.g. RS1, RS2, RS3)

RS_CONSEQ: the predicted consequences (RS-AGGT, RS-BP/BP2, RS-AGAIN, RS-DW5SS-xnt, CRYPRS-DW5SS/UP3SS-xnt), where xnt suggesting the size between the paired cryptic splice sites

RS_SCORE: the weighted confidence score of RS-site (1-5, the higher the better)

RS_POS: the first position of the essential RS-site AGGT

BP_POS: the BP position of the RS-site

PPT: the pyrimidine content in the PPT region

CLIP: if the RS-site is supported by eCLIP-U2AF data (Y/N)

RARE: if the RS-site is absent of common human variants (Y/N)

CONSERV: the averaged conservation score phyloP of the essential RS-site (numerical)

RNALM: the predicted probability by RNA language model (0-1)

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_VCF_one.py -i variants.vcf

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

    python DIVERS_VCF_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