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tjiangHIT / cuteSV

Long read based human genomic structural variation detection with cuteSV
MIT License
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cutcsv only calls indel #141

Closed HFzzzzzzz closed 8 months ago

HFzzzzzzz commented 8 months ago

Why do I use cutcsv to call vcf on my bam file, but I can only get very few vcfs, and they are all indels. In igv, it is clear that there are many small mutations. image
I used command ' cuteSV aln.end.bam Col-CEN_v1.2.fasta ERR3415821_col-0.cutesv.vcf workdir3' https://drive.google.com/file/d/1S7Q8ol-XXVCyHowBg9IzMOznVZXF39Ul/view?usp=drive_link https://drive.google.com/file/d/1RYtp84hlx8p4ZYqPdXvwUPMWk67Zhb_J/view?usp=drive_link Can you help me find out what the problem is? Is there something wrong with the bam file?

tjiangHIT commented 8 months ago

Hello @HFzzzzzzz,

Thank you for using cuteSV. Based on your description, the coverage of your aln.end.bam may be too small. Please adjust the parameter -s to above 1/6 of your coverage to increase the detection sensitivity. Besides, cuteSV focuses on identifying SVs over 30 bp at least. Hope this can help you! Best, Tao