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elixir-no-nels / rbFlow-Germline

A workflow engine with a germline calling pipeline running in a container

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Exome capture kit bed file compatibility

oskarvid opened this issue · comments

commented

NorSeq wants to use specific bed files for exome analysis, we need to make sure that these bed files are either a) compatible with the current reference file version (b37 decoy) or b) procure reference files that are compatible with the bed file.

commented

To do: Ask Rita and Tina for their exome enrichment kit bed files.

commented

To do: Ask Rita and Tina for their exome enrichment kit bed files.

They have been contacted, I am currently awaiting reply.

commented

To do: Ask Rita and Tina for their exome enrichment kit bed files.

They have been contacted, I am currently awaiting reply.

I have received bed files from both of them now.
Rita gave me the following files:

MedExome_hg38_empirical_targets.bed (43.8 MB)
MedExome_hg38_capture_targets.bed (52.6 MB)
MedExome_hg19_empirical_targets.bed (34.2 MB)
MedExome_hg19_capture_targets.bed (40.6 MB)

And Tina gave me this file:

agilent_b37_exome_v5_covered.bed (4.8MB)

I have begun poking around, will update along the way.