hisat2-extract-snps-haplotypes-vcf-py

name	hisat2-extract-snps-haplotypes-vcf-py
description	Use when extracting SNPs and haplotypes from VCF files to build variant-aware HISAT2 graph genome indexes
disable-model-invocation	true
user-invocable	true

hisat2-extract-snps-haplotypes-vcf-py

Quick Start

• Command: hisat2_extract_snps_haplotypes_VCF.py <genome_file> <VCF_fnames> <base_fname>
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/hisat2_extract_snps_haplotypes_VCF.py
• Full reference: See references/help.md

When To Use This Tool

• Use hisat2_extract_snps_haplotypes_VCF.py when your variants are already in VCF and you need HISAT2 graph-index inputs.
• It is appropriate for genome-, chromosome-, or gene-oriented reference builds where VCF-derived SNP/haplotype extraction is required.
• Use it instead of the UCSC extractor whenever the source data is generic VCF rather than UCSC SNP tables.
• Reach for --extra-files if you also want auxiliary .ref and _backbone.fa outputs for downstream inspection or genotyping workflows.

Common Patterns

# Convert one VCF into HISAT2 SNP and haplotype files
hisat2_extract_snps_haplotypes_VCF.py genome.fa variants.vcf.gz hg38_vcf

# Combine multiple VCFs via a comma-separated argument
hisat2_extract_snps_haplotypes_VCF.py genome.fa cohort1.vcf.gz,cohort2.vcf.gz hg38_vcf

# Change reference scale and emit extra backbone/reference files
hisat2_extract_snps_haplotypes_VCF.py genome.fa variants.vcf.gz hg38_vcf --reference-type chromosome --extra-files

# Allow non-rs identifiers and print extraction statistics
hisat2_extract_snps_haplotypes_VCF.py genome.fa variants.vcf.gz hg38_vcf --non-rs -v

Recommended Workflow

1. Prepare a genome FASTA file (e.g., genome.fa) and VCF file(s) containing variant data
2. Run extraction: hisat2_extract_snps_haplotypes_VCF.py genome.fa variants.vcf output_base
3. Tune --inter-gap (default: 30) and --intra-gap (default: 50) to control haplotype grouping
4. Use output files as input for HISAT2 graph index building

Guardrails

• VCF files can be plain text or gzipped; multiple files are comma-separated
• SNP IDs must begin with "rs" unless --non-rs is specified
• Use --verbose to monitor extraction statistics during processing
• Output is keyed by base_fname and writes at least .snp and .haplotype; --extra-files additionally produces .ref and _backbone.fa
• This helper does not implement --version; use -h/--help instead