Comments (1)
Code for investigation can be found on branch concordance-outliers
.
Method
For each of the outliers, calculate the concordance of the nanopore calls to the Illumina calls of all other samples.
Results
mada_2-46
This sample has perfect ALT concordance (1.0) and genome-wide concordance of 0.9999983 with mada_1-50. There were no false refs, 7 false alts, and 4 false nulls
mada_1-50
This sample had best concordance with mada_2-46
mada_1-34
This sample had best concordance with mada_1-37.
R13303 and R27006
The best concordance for these samples was actually with mada samples so it is unlikely they are sample swaps.
Conclusion
mada_2-46 and mada_1-50 seem extremely likely to be sample swaps. In addition, to have the best concordance with each other, they were sequence in the same nanopore run madagascar_tb_aug_4
. According to the spreadsheet, mada_2-46 had barcode 10 and mada_1-50 had barcode 09 - so I guess this is mixed up.
mada_1-34's best match was not on the same nanopore run so it would seem unlikely this is a sample swap. In addition, the nanopore data attached to mada_1-37 failed QC.
I will contact Simon and Sylvianne and make sure they're ok with me switching mada_2-46 and mada_1-50 barcode numbers.
The remainder I will exclude from the paper?
from head_to_head_pipeline.
Related Issues (20)
- Build AMR PRG HOT 11
- Code script to go from pandora VCF to DST result HOT 7
- Investigate R28980 & R20574 sample swap HOT 10
- Are all repeats samples clustered together HOT 9
- Mixed technology distances HOT 15
- Compare trees generated by mixed technology, with that from illumina/compass HOT 1
- Create sample resistance reference sheet HOT 1
- Get coverage info for all samples HOT 2
- Run mykrobe on all samples
- Concordance of resistance predictions with Illumina HOT 28
- Concordance of resistance predictions with phenotype HOT 15
- De novo SNP discovery in resistance genes HOT 3
- Visualise available phenotype information HOT 3
- Nanopore homopolymer deletions in katG HOT 2
- Rebasecall nanopore data with guppy v5.0.16 HOT 12
- Try mykrobe with a lower proportion of expected depth HOT 4
- Mutation concordance analysis HOT 9
- Submit data to the ENA HOT 5
- Update repository READMEs
- RIF and INH off-catalogue mutations HOT 6
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from head_to_head_pipeline.