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dellytools / delly

DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
BSD 3-Clause "New" or "Revised" License
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Delly cnv and rd.R output #367

Open ErickTong opened 8 months ago

ErickTong commented 8 months ago

Hello, I am currently using DELLY and have encountered a situation that I would like to understand better. I have run my code and observed the output, but I noticed that there are missing data points (represented as black dots) in the red-boxed area of the output image. Additionally, when I checked the corresponding coordinates in the cov.gz file, I found that there were no coordinates and CN values. Is this normal? Here is the code snippet that I ran: `delly cnv -a -u -g ref.fa -m map.fa.gz \ --window-size 10000 sample.bam \ -c cov.gz \ -o seg.bcf

bcftools query -f "%CHROM\t%POS\t%INFO/END\t%ID\t[%RDCN]\n" \ seg.bcf > segmentation.bed Rscript rd.R cov.gz segmentation.bed` And here is the output that I received: _data_Erick_Tong_02Data_analysis_project_08Genemo_vriation_call_08XHO1_leaf_variation_Tong_02call_varients_04merge_data_07cnv_rate_SCK_SCK_plot Chr01_01 My main questions are: Why are there missing data points in the red-boxed area of the image? Is it normal to have missing coordinates and CN values in the cov.gz file? How does Delly determine the intervals and calculate the CN values for CNV? I would greatly appreciate your insights on these matters. Thank you in advance for your assistance.

tobiasrausch commented 8 months ago

Probably Ns in the reference or very low mappability.