hisat2-extract-snps-haplotypes-ucsc-py

name	hisat2-extract-snps-haplotypes-ucsc-py
description	Use when extracting SNPs and haplotypes from UCSC SNP files for HISAT2 graph-based genome indexing.
disable-model-invocation	true
user-invocable	true

hisat2-extract-snps-haplotypes-ucsc-py

Quick Start

• Command: hisat2_extract_snps_haplotypes_UCSC.py <genome_file> <snp_fname> <base_fname>
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/hisat2_extract_snps_haplotypes_UCSC.py
• Full reference: See references/help.md for complete options and usage details

When To Use This Tool

• Use hisat2_extract_snps_haplotypes_UCSC.py when your variant source is a UCSC SNP table and you need HISAT2-ready .snp and .haplotype files.
• It is specifically for UCSC-formatted SNP downloads, not generic VCF input.
• Use it when preparing a variant-aware HISAT2 index from public UCSC polymorphism resources matched to a reference FASTA.
• Reach for --testset when you want synthetic reference/alternate test FASTAs alongside the normal SNP/haplotype outputs.

Common Patterns

# Convert a UCSC SNP table into HISAT2 SNP and haplotype files
hisat2_extract_snps_haplotypes_UCSC.py genome.fa snp144Common.txt.gz hg38_ucsc

# Tune haplotype grouping distances
hisat2_extract_snps_haplotypes_UCSC.py genome.fa snp144Common.txt.gz hg38_ucsc --inter-gap 30 --intra-gap 50

# Print extraction statistics to stderr
hisat2_extract_snps_haplotypes_UCSC.py genome.fa snp144Common.txt.gz hg38_ucsc -v

# Also emit testset FASTAs in addition to .snp and .haplotype
hisat2_extract_snps_haplotypes_UCSC.py genome.fa snp144Common.txt.gz hg38_ucsc --testset

Recommended Workflow

1. Download a UCSC SNP file (e.g., from hgdownload.soe.ucsc.edu/goldenPath/hg38/database/)
2. Prepare your reference genome FASTA file (genome.fa)
3. Run hisat2_extract_snps_haplotypes_UCSC.py genome.fa snp144Common.txt.gz output_base
4. Use the generated SNP/haplotype files when building a HISAT2 graph index with hisat2-build

Guardrails

• Input SNP file must be in UCSC format (plain text or gzipped); other formats are not supported
• Genome file must be a FASTA file matching the UCSC SNP file's reference build
• Use --verbose to monitor statistics; large SNP files may require significant memory
• Output is keyed by base_fname and writes at least base_fname.snp and base_fname.haplotype; --testset additionally emits .ref.testset.fa and .alt.testset.fa
• This helper does not implement --version; use -h/--help instead