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mbhall88 / head_to_head_pipeline

Snakemake pipelines to run the analysis for the Illumina vs. Nanopore comparison.
GNU General Public License v3.0
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Normalise multi-sample VCF #58

Closed mbhall88 closed 3 years ago

mbhall88 commented 3 years ago

There is actually a vital question that this issue raises: do we need the compare VCF coordinates to be aligned with H37Rv?

My initial feeling was no because that's kind of the point of compare. However, the thing that is giving me second thoughts is that it means we won't be able to mask the compare VCF.

@iqbal-lab which way do you want to go here?

mbhall88 commented 3 years ago

No normalisation will be used (for now). Given the PRG is masked during the construction phase (#55) and we lose some of the benefits of compare if we fix a reference, we won't mask the multi-sample VCF

mbhall88 commented 3 years ago

Reviving this issue, but normalising in the sense of left-aligning indels and trimming ALTs that are not called by any samples (see https://github.com/mbhall88/head_to_head_pipeline/issues/59#issuecomment-767378994)