How do I install the Vcf Phased Join skill?

Run npx skillmds add vimalinx/vcf-phased-join 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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Is Vcf Phased Join free to use?

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Who published Vcf Phased Join?

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

Vcf Phased Join by vimalinx — Agent Skill

Name: Vcf Phased Join
Rating: 4.5 (4 reviews)
Author: vimalinx

File contents

vcf-phased-join

Quick Start

Command: vcf-phased-join -o merged.vcf chunk1.vcf chunk2.vcf ...
Local executable: /home/vimalinx/miniforge3/envs/bio/bin/vcf-phased-join
Fallback launcher in this workspace: /home/vimalinx/miniforge3/envs/bio/bin/perl /home/vimalinx/miniforge3/envs/bio/bin/vcf-phased-join
Full reference: See references/help.md

When To Use This Tool

Merge overlapping pre-phased VCF chunks into one phased VCF.
Use overlap heterozygous calls to decide whether phase blocks need swapping across chunk boundaries.
Break blocks when PQ falls below a threshold with -q.
Provide a file list with -l when the chunk set is large or generated programmatically.

Common Patterns

# 1) Join three overlapping phased chunks
/home/vimalinx/miniforge3/envs/bio/bin/perl \
  /home/vimalinx/miniforge3/envs/bio/bin/vcf-phased-join \
  -o merged.vcf \
  chr1.part1.vcf chr1.part2.vcf chr1.part3.vcf

# 2) Join from a manifest file
/home/vimalinx/miniforge3/envs/bio/bin/perl \
  /home/vimalinx/miniforge3/envs/bio/bin/vcf-phased-join \
  -l chunks.txt \
  -o merged.vcf

# 3) Tighten the join criteria
/home/vimalinx/miniforge3/envs/bio/bin/perl \
  /home/vimalinx/miniforge3/envs/bio/bin/vcf-phased-join \
  -j 20 \
  -q 0.9 \
  -o merged.vcf \
  chr1.part1.vcf chr1.part2.vcf

Recommended Workflow

Confirm that all chunks are position-sorted, overlapping, and represent the same samples in the same column set.
Start with the default -j 10 and -q 0.6 thresholds unless you have a benchmarked reason to tighten them.
Write to a real output file with -o so you also capture the sidecar phase log (.plog).
Inspect the merged VCF and .plog, then validate sample ordering and phase continuity before downstream use.

Guardrails

In this shell, direct invocation may fail with Can't locate Vcf.pm; activate the bio environment first or call the script through /home/vimalinx/miniforge3/envs/bio/bin/perl.
The inputs must already be phased and overlapping; this tool does not infer phase from unphased calls.
The script warns when column names differ across files; use vcf-shuffle-cols first if sample order is inconsistent.
Output -o merged.vcf also creates merged.plog with phase-join diagnostics.
There are hidden --split-* modes in the script source, but the stable documented interface is the join workflow above.

---name: vcf-phased-joindescription: Use when joining multiple overlapping pre-phased VCF chunks into a single phased VCF using heterozygous calls from overlaps to determine correct phase.--- # vcf-phased-join ## Quick Start - **Command:** `vcf-phased-join -o merged.vcf chunk1.vcf chunk2.vcf ...` - **Local executable:** `/home/vimalinx/miniforge3/envs/bio/bin/vcf-phased-join` - **Fallback launcher in this workspace:** `/home/vimalinx/miniforge3/envs/bio/bin/perl /home/vimalinx/miniforge3/envs/bio/bin/vcf-phased-join` - **Full reference:** See `references/help.md` ## When To Use This Tool - Merge overlapping pre-phased VCF chunks into one phased VCF. - Use overlap heterozygous calls to decide whether phase blocks need swapping across chunk boundaries. - Break blocks when `PQ` falls below a threshold with `-q`. - Provide a file list with `-l` when the chunk set is large or generated programmatically. ## Common Patterns ```bash # 1) Join three overlapping phased chunks /home/vimalinx/miniforge3/envs/bio/bin/perl \ /home/vimalinx/miniforge3/envs/bio/bin/vcf-phased-join \ -o merged.vcf \ chr1.part1.vcf chr1.part2.vcf chr1.part3.vcf ``` ```bash # 2) Join from a manifest file /home/vimalinx/miniforge3/envs/bio/bin/perl \ /home/vimalinx/miniforge3/envs/bio/bin/vcf-phased-join \ -l chunks.txt \ -o merged.vcf ``` ```bash # 3) Tighten the join criteria /home/vimalinx/miniforge3/envs/bio/bin/perl \ /home/vimalinx/miniforge3/envs/bio/bin/vcf-phased-join \ -j 20 \ -q 0.9 \ -o merged.vcf \ chr1.part1.vcf chr1.part2.vcf ``` ## Recommended Workflow 1. Confirm that all chunks are position-sorted, overlapping, and represent the same samples in the same column set. 2. Start with the default `-j 10` and `-q 0.6` thresholds unless you have a benchmarked reason to tighten them. 3. Write to a real output file with `-o` so you also capture the sidecar phase log (`.plog`). 4. Inspect the merged VCF and `.plog`, then validate sample ordering and phase continuity before downstream use. ## Guardrails - In this shell, direct invocation may fail with `Can't locate Vcf.pm`; activate the bio environment first or call the script through `/home/vimalinx/miniforge3/envs/bio/bin/perl`. - The inputs must already be phased and overlapping; this tool does not infer phase from unphased calls. - The script warns when column names differ across files; use `vcf-shuffle-cols` first if sample order is inconsistent. - Output `-o merged.vcf` also creates `merged.plog` with phase-join diagnostics. - There are hidden `--split-*` modes in the script source, but the stable documented interface is the join workflow above.

Frequently asked questions