Umap

[Mame seynabou Diop]

Hello,

I need to get the uniq mappability region from my SNV file. I downloaded the Umap hg38 bed file (k100) from https://bismap.hoffmanlab.org/trackhub/.

I noticed that the region of the file overlap many segmental duplication region.

I was thinking that the regions in the umap file are uniquely mappable which is not the case for the segmental duplication. What I'm missing ? 

Thank you

[Mehran Karimzadeh]

Hello Mame,

Segmental duplications have high sequence similarity.

As long as they are not 100% identical duplications, they could still be uniquely mappable by longer reads.

Best,

Mehran

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[Mame seynabou Diop]

Hello,

Thank you fo your answer. I think then I'm in the wrong track. I want the data that will help me filter out region  where sequencing is problematic and can lead to wrong CNV calls. For that I downloaded the Umap (now from UCSC) and keep only the one with 1 as score.  After that I filter my vcf file with the Umap already filtered. I'm using the right file ?

Thank you