Unable to detect long deletions in BAM file using cuteSV / cuteFC

[linawang199210]

Hello, I found that many long deletions are clearly visible in my BAM file , but neither cuteSV nor cuteFC can detect them. Moreover, no signals are recorded in the intermediate 'sig' files (e.g., 'DEL.sigs').

cigar eg., 585S267M1D77M2I3M1D353M1500D40M1D407M1I1033M**1500D574M 、425M1I173M1D4M1D58M1500D263M2D175M1I1041M1500D**574M

• BAM file: aligned using minimap2
• cuteSV version: v2
• Reference genome: hg38 (or custom)

Best regards,
lina

[linawang199210]

样本名称不能有千分号，也就是bam的SA标签里

[Meltpinkg]

Hello, @linawang199210

The observed behavior may stem from alignment quality scores falling below cuteSV's default filtering threshold, causing the program to disregard these signatures. To conduct a thorough investigation, it would be helpful if you could share a minimal subset of the BAM file containing representative alignments exhibiting this issue, along with the complete running commands. Thank you in advance for your assistance.

Best regards,
Shuqi