LoFreq

LoFreq (SV caller)

• Author: Dreycey Albin
• Date: 05/10/2019
• Update: Dreycey (05/12/2019): finished,
• This program is used to identify structural variants
• documentation (website): lofreq GITHUB
• documentation (primary website): LOFREQ WEBSITE
• documentation (publication): https://www.ncbi.nlm.nih.gov/pubmed/23066108

Installation

INSTRUCTIONS ON HOW TO INSTALL USING TERMINAL

• installation for MacOS N/A -- not added yet
• installation for Linux

git clone https://github.com/CSB5/lofreq
cd lofreq/
./bootstrap
libtoolize
./bootstrap
./configure SAMTOOLS=/path-to-samtools HTSLIB=/path-to-htslib
make

Now typing lofreq into the terminal should work:

lofreq

ouputting the lofreq symbol and commands

OR

install binary

Basic commands

INPUT

• LoFreq can use illumina, IonTorrent, or pacbio

lofreq <command> [options]

• Commands :http://csb5.github.io/lofreq/commands/
• calling variants:

lofreq call -f ref.fa -o vars.vcf aln.bam

OUTPUT

PUT FILES HERE
GENERAL OUTPUT FROM PROGRAM (files and commands)

Example_1 -- using sniffles test set

Input files

• output files from using Bowtie (use those files)

commands

lofreq call -f GCF_000006765.1_ASM676v1_genomic.fna -o illumina_vars.vcf illumina.sorted.bam

Output files

• output is a variant calling file

illumina_vars.vcf