IVA sensitivity threshold

[antoine4ucsd]

Hi,
I am new with IVA. I am analyzing Illumina HIV data (paired end) with reads ~250-350 bp covering regions of up to ~2kb.
With my local pipeline, I cleaned up and filtered the reads and got the allele frequencies along these regions. I was willing to use IVA for reconstructing representative variants for these regions.
With the standard command, it only generated one contig. I was wondering whether I could adjust some of the options to generate less predominant variants and not only the contig?
I tried various ways (e.g. smalt_id threshold) but I got one contig only though I am expecting some diversity.
Is there anything you could suggest as parameters to adapt to get more representative /less frequent haplotypes?
Can we get the contigs relative frequencies along with the contigs themselves?

thanks!!!!

example:
iva --smalt_id 0.01 --fr Data_Interleaved.fastq Output_dir

[martinghunt]

Hi,

The aim of IVA is to collapse everything down into one contig, which should represent the most common sequence in the reads. sorry, but investigating the various alleles/variants in the sample is a separate problem that IVA is not trying to solve. I suggest mapping the reads back to the contig and go from there.

[antoine4ucsd]

thanks. I will go from there as you suggest.