No SV detection unlike other tools

[luneangevin]

Hello, I am looking to detect heterozygous SVs in an individual with a reference genome using PacBio-Hifi data. I did my mapping using minimap2, which produced sam files, which I transformed into bam, sorted and indexed, with samtools. My next script, using cuteSV, returns a VCF file containing no SV. However, the SV detection tool SVIM gives me many variants. Could the error be in my bam files? My script? Maybe I didn't take the right filters...

cuteSV --max_cluster_bias_INS 1000 --diff_ratio_merging_INS 0.9 --max_cluster_bias_DEL 1000 --diff_ratio_merging_DEL 0.5 --max_size -1 v_cardui_sorted.bam ref_v_cardui.fna cutesv_v_cardui.vcf /data/langevin/Vcf/V_cardui

Thank you in advance for your help

[Meltpinkg]

Hello, @luneangevin

You can install the newest version from pip or GitHub and have another try. In addition, the parameter "-s" represents the minimum number of reads that support a SV to be reported and the default number is 10. If the individual sequencing depth is low, the parameter should decrease to some degree. Hope it will help.

Best, Shuqi