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16 days ago
ank
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Hi, I run cnvkit using nf-core/SAREK pipeline. The start position of the results is always 0 as seen below. Is it expected? If not what my be the reason for that and how my I fix it? If expected, what does it mean?
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, 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
