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Meerkat

Meerkat is designed to identify structural variations from paired end high throughput sequencing data. It predicts structural variations from discordant read pairs then it looks for reads that cover the predicted breakpoints junctions, refines breakpoints by local alignments and predicts mechanisms that structural variations are formed.

Meerkat is available as a module on Apocrita.

Usage

To run the latest installed version of Meerkat, simply load the meerkat module:

module load meerkat

For usage documentation, run meerkat.pl -h.

Example job

Serial job

Here is an example job running on 1 cores and 2GB total memory:

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=2G

module load meerkat

pre_process.pl -b example.bam \
               -I example.fasta \
               -A example.fasta.fai

meerkat.pl -b example.bam \
           -F /path/to/reference/fasta/files


mechanism.pl -b example.bam \
             -R /path/to/repeat_mask_file

References