missing window in *cov file

[Alberto L'Abbate]

Hi Tobias,

    I'm running delly cov with the following command

delly_v0.8.7_linux_x86_64bit cnv -o $i.cnv.bcf -c $i.cov.gz -g hg38.fa -m Homo_sapiens.GRCh38.dna.primary_assembly.fa.r101.s501.blacklist.gz $i

and I noticed that in the *cov file some windows are "missed".

I mean:

chr16    14415000    14418000    2089    3.98357    1.37009
chr16    14418000    14421000    2170    5.22928    1.79853
chr16    14421000    14424000    1768    1.64356    0.565279
chr16    14424000    14427000    1669    0    0
chr16    16998000    17001000    1848    10.0533    3.45768
chr16    17001000    17004000    2352    12.7828    4.39644
chr16    17004000    17007000    1147    0    0
chr16    17007000    17010000    2253    1.45498    0.50042
chr16    17010000    17013000    2427    1.2397    0.426375

the expected is a 3kb window size, but suddenly it jumps from 14,4 MB to 16,99 Mb.
Obviously, there are other similar cases in the analysis.

Can you give me an explanation about this?

Thank you in advance.

Best,

    Alberto

[Alberto L'Abbate]

I forgot "-i 3000"

[Tobias Rausch]

Hi Alberto,

Delly requires a minimum number of mappable bases in every genomic window (-k command-line parameter). Genomic windows that are below this threshold are unreliable for copy-number estimation (e.g., windows full of Ns, non-uniquely mappable positions or extreme GC content).

Best, Tobias

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