Question: blacklist map location

[sarahdada]

Hello!

Just trying to publish something using the code:

delly cnv -g hg38_no_alt.fa
-m Homo_sapiens.GRCh38.dna.primary_assembly.fa.r101.s501.blacklist.gz chr15.bam

The issue is that I cannot find the blacklist online, can't remember where I found it, and it is missing regions ~29mbp-32mbp. That's fine but I wanted to justify why I used that- especially if the blacklist is made with short reads, and I am using long read data.

Would you know where this is, if it's worth using the blacklist for long read data, and if there would be significant changes between delly2 and delly output when using the same mappability map?

Thanks! Sarah

[tobiasrausch]

Hi Sarah, These are the standard mappability maps of delly's cnv module: https://github.com/dellytools/delly?tab=readme-ov-file#read-depth-profiles-and-copy-number-variant-calling

Best, Tobias