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Reference data: BED files, genes, transcripts, variations.
Dear Developers --
I wanted to ask how your hg19 version of CDS-canonical.bed was developed. I'd like to describe it in a reproducible way. Many thanks -- James Robert White
The link to IDT xGen Exome Research Panel v1.0 is getting redirected by IDT to the v2 product page. From there you can download the v2 bed files. There are no links to the v1 bed files on the page nor did a search turn up any links or pages to where you can still get the v1 bed files.
I have quick question re, why the number of regions would change with annotations?
wc -l
180,398 GRCh37/bed/Exome-NGv3.bed
181,166 hg19/bed/Exome-NGv3.bed
184,706 hg38/bed/Exome-NGv3.bed
Is it because some regions are not marked as gene/exonic?
Also, I downloaded a bed from roche, and the number of regions there are much larger. Could you direct me what process is used to go from vendor beds to these cleaner versions?
wget https://sequencing.roche.com/content/dam/rochesequence/worldwide/resources/SeqCapEZ_Exome_v3.0_Design_Annotation_files.zip
# SeqCap_EZ_Exome_v3_hg19_primary_targets.bed:
# This file contains the design primary target (unpadded) in hg19 coordinates and gene annotation in the 4th column.
wc -l
242,232 SeqCap_EZ_Exome_v3_hg19_primary_targets.bed
The question arises from the fact that it'd be nice to also get some Illumina BED files there for their exome sequencing kits.
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