Intra-host variant detection?
Hi,
We have quite a few high-coverage viral genome alignments (~500x) made using Mosaik and using a reference that is ~5-10% divergent to the reads. We are interested in knowing intrahost variability within a single sample by comparing differences in reads at individual bases to the consensus, NOT the reference.
Most of the available tools for that (e.g. Samtools, GATK) appear to be SNP calling based on the reference sequence and will not look for intrahost SNPs within a sample (e.g. at a single base, 80% of the reads would have an 'A', 20% would have a 'T'. If the consensus is 'A', no SNP would be called for this position - or am I wrong?).
Any suggestions for tools that could do call these intrahost variants?
Thanks a bunch.
We have quite a few high-coverage viral genome alignments (~500x) made using Mosaik and using a reference that is ~5-10% divergent to the reads. We are interested in knowing intrahost variability within a single sample by comparing differences in reads at individual bases to the consensus, NOT the reference.
Most of the available tools for that (e.g. Samtools, GATK) appear to be SNP calling based on the reference sequence and will not look for intrahost SNPs within a sample (e.g. at a single base, 80% of the reads would have an 'A', 20% would have a 'T'. If the consensus is 'A', no SNP would be called for this position - or am I wrong?).
Any suggestions for tools that could do call these intrahost variants?
Thanks a bunch.