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Some bugs found the output of the pipeline #88

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nvnieuwk opened this issue Apr 26, 2024 · 1 comment
Open

Some bugs found the output of the pipeline #88

nvnieuwk opened this issue Apr 26, 2024 · 1 comment
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bug Something isn't working
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0.2.0

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

Issues reported by @kubranarci, thank you!

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@nvnieuwk nvnieuwk added the bug Something isn't working label Apr 26, 2024
@nvnieuwk nvnieuwk added this to the 0.2.0 milestone Apr 26, 2024
@nvnieuwk
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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.

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