Mutation D232N

[Kanyerezi30]

Hello there,
We usually run hydra to produce a consensus fasta file which is later fed into the sierralocal pipeline. We realised that hydra reports D232N as N232D in the aavf file, however sierralocal captures it as D232N. D232N is a common nonpolymorphic accessory mutation selected in persons receiving RAL and EVG. Alone, it has little effect on INSTI susceptibility.

On further interrogation, we found out that it (D232N) is not even included in the mutation_db.tsv. How best can we rectify this

In addition, we request to be advised on how we can update the mutation_db.tsv in future.

[ericenns]

Hi, hydra does not report variants in the AAVF file as the format you specified. For example it looks like below.

#CHROM	GENE	POS	REF	ALT	FILTER	ALT_FREQ	COVERAGE	INFO
hxb2_pol	RT	48	S	*	af0.01	0.0031	324	RC=tca;AC=tAa;ACF=0.0031;CAT=.;SRVL=.

I also inspected our reference which is hxb2 and at position 232 in Integrase the reference base is N composed of the nucleotides AAT. This matches the latest version of HIV-1 hxb2 that is on NCBI (https://www.ncbi.nlm.nih.gov/nuccore/K03455.1?report=fasta&from=2253&to=5096).

Updating the built in mutation database is not straightforward as Stanford HIVDB does not have this info available in an easy format for us to parse and generate a new file. For this, I recommend uploading your AAVF to this program and run it for analysis https://hivdb.stanford.edu/hivdb/by-reads/.

[Kanyerezi30]

Thanks @ericenns,
I agree with you about the format.
We shall cross check with Stanford HIVDB too as recommend. Though from the screenshot below, it seems they have D as their reference but we shall further see how to compare with our aavf