mbhall88
commented
3 years ago After thinking through a number of options for going from a Pandora VCF to a prediction, the method I have decided to pursue (at least initially - it may turn out to not work) is outlined below.
- Filter the Pandora VCF: I don't think this requires much explanation and I will (initially) go with the filtering used in #48
- Load Pandora VCF entries with an ALT genotype called into a HashMap where the key is a tuple of
(gene, interval)whereintervalis the start/end range of the variant. This key will map to the VCF entry. A side note: we will also load filtered variants and make predictions on them, but keep those predictions will only be for debugging/investigative purposes. This will likely be useful for a multitude of reasons. - Loop over each variant in the panel VCF. Collect all Pandora variants for the same gene, whose interval has an intersection with the panel variant's interval. The advantage here is that we "seamlessly" handle when Pandora has merged panel variants in the PRG. For those intersecting Pandora variants, we look at the intersection interval and see whether the Pandora variant matches any of the panel variant ALTs. If it does match a panel variant ALT, we add an annotation to the VCF INFO field (say a tag called prediction) and write out an annotated version of the Pandora VCF, along with a mykrobe-style JSON.
One advantage of this approach is it removes the need to add another external dependency (bcftools) and also removes the need to deal with ORFs when trying to translate the Pandora consensus.
An example of how the comparison of the intersecting intervals will work is
We have panel variants
#CHROM POS ID REF ALT INFO
gid 4 gid_M2I ATG ATA,ATC,ATT DRUGS=drug1,drug2
gid 7 gid_L3F TTA TTC,TTT DRUGS=drug3
gid 20 gid_A20C A C drugs=drug4and a Pandora variant
#CHROM POS ID REF ALT ... FORMAT sample
gid 3 . CATGTTAT CATCTTAT,CATGTTCT . GT 1The interval for the Pandora variant is [3, 11). So, for the first panel variant, we get an intersection interval of [4, 7). This interval on the called Pandora allele is ATC, which matches one of the panel variant ALT alleles, so we say this panel variant, gid_M2I, is present. For the next panel variant, the intersection interval is [7, 10). This interval on the called Pandora allele is TTA, which matches the panel variant REF, so we say it is not present. The third panel variant's interval does not intersect with the pandora variant, so we skip it. In the end, we say this sample is resistant to drug1 and drug2, due to variant gid_M2I
iqbal-lab
The first main step in producing resistance predictions is running
pandora mapon the AMR PRG (#66) with the reads.The first attempt at this, I (randomly) picked sample
R28581. The mykrobe call for this sample on both Illumina and Nanopore was resistant to Isoniazid, with variantkatG_W191Rand has a lot of supporting coverage.The pandora genotyped VCF, selecting only alt calls
and trimming the unused alt alleles
using the current filtering strategy, the first variant, at position 523, would be filtered due to low FRS. The second variant would be kept.
The encouraging thing is if we look at that position in the panel VCF, the entry is
which is the variant we expect to find