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cnvkit result start position is always 0. What might be the reason? #931

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altayg opened this issue Dec 6, 2024 · 0 comments
Open

cnvkit result start position is always 0. What might be the reason? #931

altayg opened this issue Dec 6, 2024 · 0 comments

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@altayg
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altayg commented Dec 6, 2024

Hi, I run cnvkit using nf-core/SAREK pipeline. The start position of the results is always 0. Is it expected? If not what my bey the reason for that and how mya I fix it? The below is the example head portion of the cnvkit result using sarek over one of my ctDNA samples with file extension Sample1.md.cns. Because the start position of the results is always 0, during the annotation process (using AnnotSV downstream as sarek annotation does not work for cnvkit), I see around 5K genes per cnv call like a chromosome level event and this looks not ok to me.
chromosome start end gene log2 depth probes weight ci_lo ci_hi
chr1 0 215956422 - 0.213308 0.256061 1 1 0.233308 0.233308
chr2 0 299993529 - 0.338876 0.264308 1 1 0.398876 0.398876
chr3 0 104445559 - -0.181945 0.189516 1 1 -0.191945 -0.181945

Could you please help with this issue?

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