* g++ compiler
* CMake
* GNU awk and core utils
* BWA (http://bio-bwa.sourceforge.net/)
* Samtools (0.1.18+) ([htslib.org/](http://www.htslib.org/))
* SAMBLASTER (0.1.19+) ([github repo](https://github.com/GregoryFaust/samblaster))
* Python 2.7 ([python.org/](https://www.python.org/)) with pysam (0.8.3+), NumPy (1.8.1+) and scipy (1.2.1+)
* Vawk (https://github.com/cc2qe/vawk)
* sambamba ([gihub repo](https://github.com/lomereiter/sambamba))
* gawk ([GNU project](https://www.gnu.org/software/gawk/))
git clone --recursive git@github.com:arq5x/lumpy-sv.git
cd lumpy-sv
make
cp bin/* /usr/local/bin/.
pip install git+https://github.com/hall-lab/svtyper.git
# Align paired-end reads to Reference
bwa mem -R "@RG\tID:id\tSM:sample\tLB:lib" reference.fasta sample.R1.fastq sample.R2.fastq \
| samblaster --excludeDups --addMateTags --maxSplitCount 2 --minNonOverlap 20 \
| samtools view -Sb - \
> sample.bam
# Extract the discordant paired-end alignments from BAM file
samtools view -b -F 1294 sample.bam > sample.discordants.unsorted.bam
# Extract the split-read alignments from BAM file
samtools view -h sample.bam \
| scripts/extractSplitReads_BwaMem -i stdin \
| samtools view -Sb - \
> sample.splitters.unsorted.bam
# Sort discordant and splitters bam files
samtools sort sample.discordants.unsorted.bam -o sample.discordants.bam
samtools sort sample.splitters.unsorted.bam - o sample.splitters.bam
# Run LUMPYEXPRESS on a single sample with pre-extracted splitters and discordants
lumpyexpress -P -B sample.bam -S sample.splitters.bam -D sample.discordants.bam -o sample.vcf
# Genotyping individual samples with SVTyper
svtyper -B sample.bam -i sample.vcf -l sample.bam.json > sample.gt.vcf
# Sorting,compressing and indexing VCF files
vcf-sort sample.gt.vcf > sample_sorted.gt.vcf
bgzip sample_sorted.gt.vcf
tabix sample_sorted.gt.vcf.gz
# Run SVTOOLS LSORT to combine and sort variants from multiple samples
svtools lsort sample1_sorted.gt.vcf.gz sample2_sorted.gt.vcf.sample3_sorted.gt.vcf.gz \
| bgzip -c > sorted.vcf.gz
# Run SVTOOLS LMERGE to merge variant calls likely representing same variant in the sorted VCF
zcat sorted.vcf.gz | svtools lmerge -i /dev/stdin -f 20 | bgzip -c > merged.vcf.gz
# Run SVTOOLS GENOTYPE to genotype all samples present in the merged set
mkdir -p gt
zcat merged.vcf.gz | vawk --header '{ $6="."; print }' | svtools genotype -B sample.bam -l sample.bam.json \
| sed 's/PR...=[0-9\.e,-]*\(;\)\{0,1\}\(\t\)\{0,1\}/\2/g' - > gt/final.vcf
https://github.com/HancockLab/SVs_in_1301_A.thaliana_lines_Main_Figures