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elixir-no-nels / rbFlow-Germline

A workflow engine with a germline calling pipeline running in a container
MIT License
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Exome capture kit bed file compatibility #20

Open oskarvid opened 5 years ago

oskarvid commented 5 years ago

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.

oskarvid commented 5 years ago

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

oskarvid commented 5 years ago

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

They have been contacted, I am currently awaiting reply.

oskarvid commented 5 years ago

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.