Common SNP/variome-aware restriction digest generator for human genome

Question

[hurfdurf]

Hi community:

Is there a tool already written that will simulate restriction enzyme cuts in a genome sequence file, AND also emits potential restriction enzyme digests found in a common SNP database for humans? The goal is to find fragmentation strategies that will be relatively insensitive to SNPs and generate an acceptable size distribution across several loci of interest.

I'm aware of existing digesters like hicup_digester (https://github.com/StevenWingett/HiCUP/blob/master/hicup_digester) but it doesn't cover SNP expansion.

I know this is medium-complicated to code up but don't want to reinvent the wheel if a better well tested version already exists. Ideal output would be BED-ish coordinates of all the sites perhaps scored by population VAF if they are SNP-associated.

Answer 1

[Pierre Lindenbaum]

pipe your SNP database as a VCF file into vcfrebase: https://jvarkit.readthedocs.io/en/latest/VcfRebase/

java -jar jvarkit.jar vcfrebase -R ref.fa dbsnp.vcf