Run pbsv to call SVs

Due to the tool transposition_deTEct only takes structural variant detected by either pbsv or sniffles, we run pbsv.

Data type

It has to be long-read DNA data!

Installation

conda activate py38_deTEct
conda install -c bioconda pbsv
conda install pbmm2 # The recommended aligner

Usage

conda activate py38_deTEct
REF=/media/XLStorage/ybao2/RefGenome/dmel-all-chromosome-r6.39.fasta
fq=/media/XLStorage/ybao2/Jimmy_data/TEST_deTEct/test.fq.gz
bam=/media/XLStorage/ybao2/Jimmy_data/TEST_deTEct/test.bam
sample=testSample
out=/media/XLStorage/ybao2/Jimmy_data/TEST_deTEct

# 1. Align reads to a reference genome
pbmm2 align $REF $fq $bam --sort --sample $sample
# 2. Discover signatures of structural variation
pbsv discover $bam $out/$sample.svsig.gz
# optionally index svsig.gz to allow random access via `pbsv call -r`
tabix -c '#' -s 3 -b 4 -e 4 $out/$sample.svsig.gz
# 3. Call structural variants and assign genotypes
pbsv call $REF $out/$sample.svsig.gz $out/$sample.ref.var.vcf