Requires Novoalign v3.02.10 or higher. Please download from www.novocraft.com and request a free license key if you're not a licensed user as yet.
- Bedtools (2.15 or higher) https://github.com/arq5x/bedtools2
- Samtools (0.1.18 or higher)
- bcftools (latest) See http://samtools.github.io/bcftools
- tabix and bgzip (for VCF files)
- GNU parallel
All the dependencies must be in the UNIX $PATH
Run from the UNIX command line.
Works for paired-end reads only Requires amplicon definitions
Run as the following
bash novoamplicon/code/runApp.sh 1111 NA12878-AFP1_S17_L001_R1_001.fastq.gz NA12878-AFP1_S17_L001_R2_001.fastq.gz genome.fa novoamplicon/t/truseq_amplicon_cancer_panel_manifest_afp1_pn15032433_b.txtbash novoamplicon/code/runApp.sh <sid> <read1.fastq> <read2.fastq> <reference.fasta> <manifest_file>
An output directory named by sample ID