SURVIVOR(1)

🎀 SURVIVOR(1) 🎀

Okay bestie, the manual name is SURVIVOR and it lives in the User Commands section 💅 Let's make this page actually slay ✨

🌸 NAME 🌸

SURVIVOR - <short_description> 🫶 The one-line blurb is still just the <short_description> placeholder, so this is where it goes.

🦋 SYNOPSIS 🦋

SURVIVOR <command> [options]

Pick a command, toss in whatever options you want, and you're off 🧚

💜 DESCRIPTION 💜

Program: SURVIVOR (Tools for Structural Variations in the VCF format) 🍓 Version: 1.0.6 ⭐

Here's the full squad of commands, grouped by vibe:

🧪 Simulation/ Evaluation

• simSV — Simulates SVs and SNPs on a reference genome 🧬
• scanreads — Pulls error profiles out of mapped reads so your simulation has realistic errors 🔍
• simreads — Simulates long reads (Pacio or ONT) 📖
• eval — Evaluates a VCF file after SV calling over simulated data 📊

🔍 Comparison/filtering

• merge — Compares or merges VCF files to make a consensus or multi sample VCF files 🤝
• genComp — Generates a pairwise comparison matrix based on any multi sample VCF file 🪞
• filter — Filters a VCF file based on size and/or regions to ignore 🧹
• stats — Reports multiple stats over a VCF file 📈
• compMUMMer — Annotates a VCF file with the breakpoints found with MUMMer (Show-diff) 🔬

🔁 Conversion

• bincov — Bins a coverage vector into a bed file so you can filter SVs in low MQ regions 🗂️
• vcftobed — Converts a VCF file to a bed file 🔄
• bedtovcf — Converts a bed file to a VCF file 🔄
• smaptovcf — Converts the smap file to a VCF file (beta version) 🧪
• bedpetovcf — Converts a bedpe file to a VCF file (beta version) 🧪
• hapcuttovcf — Converts the Hapcut2 final file to a VCF file using the original SNP file you gave Hapcut2 💫
• convertAssemblytics — Converts Assemblytics to a VCF file 🌈

👑 AUTHOR 👑

This manpage was written by Nilesh Patra for the Debian distribution, and it can be used for any other usage of the program 💖

SURVIVOR 1.0.6 from September 2020, SURVIVOR(1) 🦋 that's the whole page, bestie, go be iconic 💜✨