Question: Possible to call variants from PacBio reads from a mixed sample?
gravatar for nchuang
7 months ago by
United States
nchuang200 wrote:

For whatever reason my PI decided to submit many long amplicons for PacBio sequencing without barcoding each amplicon. He now wants to know how much variation exists between the samples. I was looking at the Long Amplicon Analysis (LAA) tool and it says it can generate consensus based on unique individual molecules. I don't know if it can account for each molecule without barcoding.

Is there a way to call variation on this mixed sample file? I already did a simple bam-readcount and it gives too many possible variants at each site. I figured I need a true variant caller to distinguish true variants. Samtools/Bcftools mpileup basically stalls out with nothing written to file. I am assuming it can't handle the long reads.

snp pacbio long reads • 248 views
ADD COMMENTlink written 7 months ago by nchuang200
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