Missing access hg38 bed file

[ashwini06]

Hi,

I am looking for hg38 accessible bed file (access-5k-mappable.hg38.bed) in https://github.com/etal/cnvkit/tree/master/data and is missing. Can you please update it for downloading from data/ or instruct me for generate this file ?

Thank you!

[yulijia]

Hi,
You could use cnvkit.py access command to generate any sequence-accessible coordinates file by yourself.
Please see this page
https://cnvkit.readthedocs.io/en/stable/pipeline.html#access

Calculate the sequence-accessible coordinates in chromosomes from the given reference genome, output as a BED file.

cnvkit.py access hg19.fa -x excludes.bed -o access-excludes.hg19.bed
cnvkit.py access mm10.fasta -s 10000 -o access-10kb.mm10.bed

[stroke1989]

@yulijia
Hi,
to generate sequence-accessible coordinates file, a file of regions of poor mappability is needed. Where I can get this file for hg38? Hope your response!

[awast]

Hello Sir stroke1989
If you have any update regarding generation of this file please share....

[yulijia]

@stroke1989 @awast

Please see this post to find the the mappability file
https://www.biostars.org/p/487547/

[awast]

@stroke1989 @awast

Please see this post to find the the mappability file https://www.biostars.org/p/487547/

Thankyou Sir..

[etal]

CNVkit now ships an hg38 accessible-regions file, data/access-10kb.hg38.bed (added alongside the hg38 refFlat data), and it's used throughout the hg38 examples in the documentation. For a mappability-filtered access file, the Pipeline documentation describes generating one with cnvkit.py access hg38.fa -x <excludes>.bed and links the UCSC hg38 mappability tracks for building the exclude list. Between the shipped 10kb file and the access command, the hg38 gap reported here is covered, so closing. (A pre-built access-5k-mappable.hg38.bed asset like the hg19 one isn't bundled yet — if that specifically would help, let us know.)