How do I install the Hisat2 Extract Snps Haplotypes Ucsc Py skill?

Run npx skillmds add vimalinx/hisat2-extract-snps-haplotypes-ucsc-py in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

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vimalinx (@vimalinx) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Hisat2 Extract Snps Haplotypes Ucsc Py by vimalinx

Name: Hisat2 Extract Snps Haplotypes Ucsc Py
Rating: 4.2 (5 reviews)
Author: vimalinx

File contents

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

Download a UCSC SNP file (e.g., from hgdownload.soe.ucsc.edu/goldenPath/hg38/database/)
Prepare your reference genome FASTA file (genome.fa)
Run hisat2_extract_snps_haplotypes_UCSC.py genome.fa snp144Common.txt.gz output_base
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

---name: hisat2-extract-snps-haplotypes-ucsc-pydescription: Use when extracting SNPs and haplotypes from UCSC SNP files for HISAT2 graph-based genome indexing.--- # 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](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 ```bash # 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

Frequently asked questions