Variants smaller than threshold set

[Akazhiel]

Hello,

I was running cuteSV and I came across something odd. I had set the minimum variant length to 30bp but found insertions as short as 10bp.

This was the command I used to run it:

cuteSV -t 40 -S CUTESV_Tumor -l 30 -s 2 -L -1 -md 5 --retain_work_dir --genotype --max_cluster_bias_INS 50 --diff_ratio_merging_INS 0.3 --max_cluster_bias_DEL 50 --diff_ratio_merging_DEL 0.3 --remain_reads_ratio 0.8 GROS_14_Tumor.bam /input/GRCh38.d1.vd1.fa CUTESV_Tumor.vcf cutesv_tumor/

[tjiangHIT]

Hello @Akazhiel,

Thank you for putting forward this strange but interesting issue.
In our practice, we have not encountered a case like this.
Could you provide a small bam file covering this case for us in order to reproduce the issue and debug it?
I will appreciate it if you can supply it. My email is tjiangAThitDOTeduDOTcn.

Thank you in advance.
Tao