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# Indel Marker Detector
This Python script detects unique indel markers from multiple VCF files for two different strains. It uses the `pysam` library to read VCF files and the genome file, and the `argparse` library to handle command-line arguments.

## Requirements
- Python 3
- pysam library

## Usage
Run the script with the following command:

python indel_marker_detector.py --strain1 indel_file1.vcf.gz indel_file2.vcf.gz --strain2 indel_file3.vcf.gz indel_file4.vcf.gz --genome genome.fa

## Command-Line Arguments
- `--strain1`: Specify one or more VCF files for strain 1.
- `--strain2`: Specify one or more VCF files for strain 2.
- `--genome`: Specify the genome file.

## Output
The script outputs two CSV files, `strain1_markers.csv` and `strain2_markers.csv`, which contain the detected indel markers for strain 1 and strain 2, respectively. Each row in the CSV files represents a marker and includes the following columns: Chromosome, Marker Start, Marker End, Indel Position, Marker Sequence, Indel Sequence.

## Here is a brief description of the script and its command-line arguments:
usage: indel_marker_detector.py --strain1 VCF_FILES [VCF_FILES ...] --strain2 VCF_FILES [VCF_FILES ...] --genome GENOME_FILE

This script detects unique indel markers from multiple VCF files for two different strains.

optional arguments:
  --strain1 VCF_FILES [VCF_FILES ...]
                        Specify one or more VCF files for strain 1.
  --strain2 VCF_FILES [VCF_FILES ...]
                        Specify one or more VCF files for strain 2.
  --genome GENOME_FILE
                        Specify the genome file.