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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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Assign lineages for project samples #26

Closed mbhall88 closed 4 years ago

mbhall88 commented 4 years ago

This information will not doubt be useful at some point.

For now, probably easiest to use the lineage assignment script from the PRG building and the VCFs from COMPASS.

mbhall88 commented 4 years ago

An overall view of the lineage assignments (individual assignments will be in the QC report).

This is with 1 het. call allowed (i.e. two or more het calls result in a mixed call).

Major

     36 1
     61 2
     10 3
     62 4
      4 mixed
      5 unknown

Full

     34 1.1.2
      2 1.2.2
     23 2.2
     26 2.2.1
      1 2.2.3
      3 2.2.6_RD150
      8 2.2.7
     10 3.1.1
      3 4
     17 4.10
     11 4.1.1.3
      3 4.1.2
     10 4.1.2.1
      3 4.1.3
      2 4.3.2.1
      1 4.3.3
      1 4.3.4.2.1
      6 4.4.1.1
      1 4.6.2.1
      4 4.6.2.2
      4 mixed
      5 unknown

cc @iqbal-lab

mbhall88 commented 4 years ago

Individual assignment CSV files are located in /hps/nobackup/research/zi/projects/tech_wars/data/QC/report/lineage_assignment

iqbal-lab commented 4 years ago

Figure 1 here might be useful background in terms of what we expect https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0200632