pbsv.md

The installation and usage of PBSV

1. About

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

2. Installation and Usage

mamba

mamba install -c bioconda PBSV=2.8.0

2.1 Reads mapping

minimap2 -ax map-hifi --MD -t 16 -Y -R '@RG\tID:SRR11951494\tPL:pacbio\tLB:library\tSM:SRR11951494' /home/qgn1237/qgn1237/1_my_database/GRCh38_p13/minimap2_index/GRCh38.p13.genome.mmi /projects/b1171/qgn1237/2_raw_data/smooth_seq_95_sc_K562_SMRT/SRR11951494/SRR11951494.fastq | samtools sort -@ 16 -m 2G -O BAM -o PC3.bam && samtools index PC3.bam PC3.bai

2.2 Discover signatures

It is highly recommended to provide one tandem repeat annotation .bed file of your reference to pbsv discover via --tandem-repeats. This increases sensitivity and recall.

pbsv discover --tandem-repeats ~/qgn1237/1_my_database/GRCh38_p13/tandem_repeats/human_GRCh38_no_alt_analysis_set.trf.bed ./SRR11951439_sort.bam ./SRR11951439_sort.svsig.gz

2.3 Call structural variants and assign genotypes

For pacbio

pbsv call --ccs -j 6 ~/qgn1237/1_my_database/GRCh38_p13/GRCh38.p13.genome.fa /home/qgn1237/qgn1237/4_single_cell_SV_chimera/1_smooth_seq_95_sc_K562_SMRT/SRR11951439/SRR11951439_sort.svsig.gz /home/qgn1237/qgn1237/4_single_cell_SV_chimera/1_smooth_seq_95_sc_K562_SMRT/SRR11951439/SRR11951439_sort.var.vcf

For nanopore

pbsv call --ccs -j 6 ~/qgn1237/1_my_database/GRCh38_p13/GRCh38.p13.genome.fa /home/qgn1237/qgn1237/4_single_cell_SV_chimera/1_smooth_seq_95_sc_K562_SMRT/SRR11951439/SRR11951439_sort.svsig.gz /home/qgn1237/qgn1237/4_single_cell_SV_chimera/1_smooth_seq_95_sc_K562_SMRT/SRR11951439/SRR11951439_sort.var.vcf

-j means threads

2.4 Output files

SRR11951439_sort.var.vcf