Known SV not detected in final output

[mzwaig]

Hello,

I'm using CuteSV on Nanopore data with 30X coverage. My sample has a known duplication that isn't making it into the final output but it is detected in the signatures file. I was wondering if you could recommend alternative parameters which could help me catch it. Here's what I've been using. I know it is supported by 7 reads all with a MAPQ of 60.

Thanks, Melissa

cuteSV $BAM $REF ${PROJDIR}/CuteSV/${Sample}/${Sample}.CuteSV.vcf ${PROJDIR}/CuteSV/${Sample}/ \
			-S ${Sample} \
			--max_size 3000000 \
			--min_support 1 \
			--max_cluster_bias_INS 100 \
			--diff_ratio_merging_INS 0.3 \
			--max_cluster_bias_DEL 100 \
			--diff_ratio_merging_DEL 0.3 \
			 --retain_work_dir --report_readid

DUP	chr7	138861117	140782817	9aec5e38-c0aa-4005-b0b6-3da9ac1da2fd
DUP	chr7	138861117	140782817	e5e61d25-4c36-4bfb-8b8c-87ea6b6f42e1
DUP	chr7	138861117	140782817	e97c7c35-5587-4ef1-94fd-46065cf536b0
DUP	chr7	138861117	140782817	76cfe648-35c1-4662-b940-44436c05a5a5
DUP	chr7	138861117	140782817	2900cb39-6002-4cd1-8cea-de34d070e6a5
DUP	chr7	138861118	140782816	5473d280-3c0e-4e84-a20a-adaf4f5218d3
DUP	chr7	138861121	140782815	c60e972c-0743-4478-b23d-395b5b82c600

[Meltpinkg]

Hello Melissa,

Thanks for pointing this out. Could you please supply a part of your data which covers the missing DUP for me to check the error? You can use these commands to extract data as below:

samtools view -H $BAM chr7:138810000-140830000 > test.sam 
samtools view -buS test.sam | samtools sort -O bam > test.bam 
samtools index test.bam 

Please send test.bam and test.bam.bai to me via [email protected] or [email protected].

Best, Shuqi

[zhemingfan]

Hi Shuqi,

I'm having the same issue as @mzwaig , albeit for tandem duplications, I will look into sending you the data.

Thanks, Jeremy