HyINDEL

Installation

Requirements

Tested with GCC (minimum tested version 4.9.2 check using gcc -v), C++11 support required

• CMake
• Minia
• Minimap2
• Mosdepth
• Samtools

git clone --recursive https://github.com/alok123t/HyINDEL.git
cd HyINDEL && mkdir -p build && cd build
# with root access
cmake .. && make -j 4 install

# without root access, install in a local directory
# Executable path will be /path/to/install/dir/bin/HyINDEL
mkdir -p /path/to/install/dir
cmake .. -DCMAKE_INSTALL_PREFIX=/path/to/install/dir && make -j 4 install

Note:

• Make sure paths to minia, minimap2, mosdepth and samtools are on PATH, otherwise write the absolute paths before installation in scripts/Assemble.sh, scripts/Pre.sh and scripts/Post.sh
• Will install/replace bamtools if already present in installation directory

Usage

HyINDEL --help

Test Example

HyINDEL -i ../test/input.bam -o ../test/output -r ../test/ref.fa -s 350 -d 20 -l 100 -c 30 -t 4

Compare output with file test/expected-output.vcf

Input/Output

• Input file: Coordinate sorted BAM file with index (.bai)
• Output file: output.vcf in output directory

Output directory will be created, if it doesn't exist

Parameters

Options Short	Options Long	Description	Attributes	Mandatory
-i PATH	--inp=PATH	Input File	Path	[x] yes
-o PATH	--out=PATH	Output Folder	Path	[x] yes
-s VAL	--insSz=VAL	Insert Size	Integer	[x] yes
-d VAL	--stdDev=VAL	Standard Deviation	Integer	[x] yes
-l VAL	--readLen=VAL	Read Length	Integer	[x] yes
-c VAL	--cov=VAL	Coverage	Integer	[x] yes
-t VAL	--threads=VAL	Threads	Integer	[ ] no