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
mamba install -c bioconda PBSV=2.8.0
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
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
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
SRR11951439_sort.var.vcf