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Missing lower CIPOS and CIEND from CNVkit #72

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khurrammaqbool opened this issue Oct 9, 2024 · 0 comments
Open

Missing lower CIPOS and CIEND from CNVkit #72

khurrammaqbool opened this issue Oct 9, 2024 · 0 comments

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@khurrammaqbool
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khurrammaqbool commented Oct 9, 2024

SVDB is wrongly parsing the CIPOS and CIEND from CNVkit VCF output leading to missing lower bounds for CIPOS and CIEND. The example is given below:

CNVkit:
1       10500   .       N       <DEL>   .       .       IMPRECISE;SVTYPE=DEL;END=121484934;SVLEN=-121474434;FOLD_CHANGE=1.0641951251709667;FOLD_CHANGE_LOG=0.0897627;PROBES=1327;CIPOS=(0,166417);CIEND=(160417,194588) GT:GQ   0/1:1327

SVDB:
1       10500   .       N       <DEL>   .       .       IMPRECISE;SVTYPE=DEL;END=121484934;SVLEN=-121474434;FOLD_CHANGE=1.0642;FOLD_CHANGE_LOG=0.0897627;PROBES=1327;CIPOS=.,166417;CIEND=.,194588;set=cnvkit;FOUNDBY=1;cnvkit_CHROM=.|1;cnvkit_POS=.|10500;cnvkit_QUAL=.|.;cnvkit_FILTERS=.|.;cnvkit_SAMPLE=.|TUMOR|GT:0/1|GQ:1327;cnvkit_INFO=.|..(trimmed ......)

```
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