Compatibility with bed file is provided that contains 1,000,000 random positions on the hg19/GRCh37 human genome reference ?

mroosmalen / nanosv

SV caller for nanopore data

MIT License

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Compatibility with bed file is provided that contains 1,000,000 random positions on the hg19/GRCh37 human genome reference ? #80

Open ElisouG opened 1 month ago

ElisouG commented 1 month ago

Hi nanosv team, Is your tool compatible with human genome version hg38/GRCh378 ? If yes, did you produce the bed file for compute the coverage distribution with this genome and could you share it ? If not, how can I generate it ? Kind regards, Elise

SouvilleL commented 2 weeks ago

Hi Elise,

To generate a random bed file, you can use bedtools random command. I use it when i am working with custom reference, it seems to be working without problem. bedtools random -l 1 -seed 1251 -g ref.fai > random.bed

Louis