cymbopogon/pbsv repository overview

⁠pbsv

pbsv is a suite of tools to call and analyze structural variants in diploid genomes from PacBio single molecule real-time sequencing (SMRT) reads. The tools power the Structural Variant Calling analysis workflow in PacBio's SMRT Link GUI.

pbsv calls insertions, deletions, inversions, duplications, and translocations. Both single-sample calling and joint (multi-sample) calling are provided. pbsv is most effective for:

• insertions 20 bp to 10 kb
• deletions 20 bp to 100 kb
• inversions 200 bp to 10 kb
• duplications 20 bp to 10 kb
• translocations between different chromosomes or further than 100kb apart on a single chromosome

⁠Run me

INPUT_DIR=/path/to/input
OUTPUT_DIR=/path/to/output

BAM=ref.movie1.bam
OUTPUT_SVSIG=ref.sample1.svsig.gz

docker run --rm \
-v "${INPUT_DIR}":"${INPUT_DIR}" \
-v "${OUTPUT_DIR}":"${OUTPUT_DIR}" \
cymbopogon/pbsv:2.6.2 discover \
"${INPUT_DIR}/${BAM}" \
"${OUTPUT_DIR}/${OUTPUT_SVSIG}"