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The provided script is a Python program that 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.

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CaiBiotech/Indel-Marker-Detector

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5d00439 · Jun 30, 2023

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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.

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The provided script is a Python program that 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.

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