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Cram without provided reference causes undetected failure #149

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illusional opened this issue Jun 27, 2022 · 0 comments

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bug

illusional commented Jun 27, 2022

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Describe the bug

There are not many variants for OHMR4 in seqr. Through investigation by @vladsaveliev + @lgruen, it was discovered that:

We were provided CRAMs
We did not link the provided reference to the crams
Bazam is failing because it can't correctly realign without the original reference
The failure was obscured due to process substitution (code)
Re-aligned CRAMs look small

Resolution

The resolution is to:

Make SM record the assigned reference when input type is CRAM: Add reference assembly as requirement for crams metamist#242
Ensure production-pipelines uses this new reference for crams: Add 'reference_assembly' to bazam from SMDB production-pipelines#71

illusional added the bug label

illusional assigned lgruen and illusional

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