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HuiyangYu / PanDepth

An ultra-fast and efficient genomic tool for coverage calculation
https://github.com/HuiyangYu/PanDepth
MIT License
128 stars 4 forks source link

distinguish with unaligned region and deletion region #4

Closed baozg closed 5 months ago

baozg commented 5 months ago

Hi, @HuiyangYu

Thanks for this super-fast tool. Is it possible to distinguish between the unaligned region (not in PAF) and deletion (D in the CIGAR) in the whole genome alignment?

HuiyangYu commented 5 months ago

Thank you very much for your appreciation of PanDepth. However, I regret to inform you that our tools may not directly meet your requirements. I am unsure whether you are looking for deletion type structural variants or have other specific needs. If it is the former, you may consider using tools such as Manta (short reads), cuteSV (long reads), paftools (genome), among others. For specialized requirements, you can temporarily utilize the ' -w ' parameter in PanDepth and set it to 50, 100, or other window size (bp). Regions with the coverage of 0 indicate unaligned region or deletion.

baozg commented 5 months ago

No, I don't want to call variants from PAF. But I am curious what's the exact meaning of coverage 0 in the PAF. I think I could go back to the origanl PAF and use their coordinate as aligned region. If one deletion in the CIGAR, then PanDepth counts this region as 0, right?

HuiyangYu commented 5 months ago

The coverage of 0 indicates that this genomic region lacks any read/genome aligned, or that all reads/genome in this region are completely covered by a deletion.

baozg commented 5 months ago

Thank you for the clarification.