Some bugs found the output of the pipeline

[nvnieuwk]

Description of the bug

1. wisecondorx reports SVLEN wrong I guess:

chr21	13900001	wisecondorx_344	N	<DEL>	.	PASS	CNV_RATIO=-0.0368;ZSCORE=-8.95856;SVTYPE=CNV;END=24100000;SVLEN=1;CALLERS=wisecondorx	GT:CN	.:0
chr21	24100001	wisecondorx_345	N	<DUP>	.	PASS	CNV_RATIO=0.1254;ZSCORE=23.8602;SVTYPE=CNV;END=25700000;SVLEN=1;CALLERS=wisecondorx	GT:CN	.:0

2. not sure if this is a bug or not but in qdnaseq tool thereis only result for chr18,chrX and chrY
3. SVLEN is missing in DELLY

Issues reported by @kubranarci, thank you!

Command used and terminal output

No response

Relevant files

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System information

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[nvnieuwk]

The first issue is a bug in bedgovcf which has been fixed in version 0.1.1. I'll update the version in the pipeline.