hmm, I just saw this too, quiver only calls haploid variants. My data is human. The reason to use pacbio ccs instead of illumina is that we want to find some really low freq small indels. We think CCS should be much more accurate.
So can I use Plurality? Or do I have to go back to GATK? It seems that the gatk module in smrtanalysis pipeline cannot find indels.
So you suggest using compareSequences.py instead of blasr?
Once I get alignment from blasr as sam files, could I just leave smrtanalysis modules and use GATK or samtools to call variants? But still I don't know how different it will be compared to illumina reads.
So can I use Plurality? Or do I have to go back to GATK? It seems that the gatk module in smrtanalysis pipeline cannot find indels.
So you suggest using compareSequences.py instead of blasr?
Once I get alignment from blasr as sam files, could I just leave smrtanalysis modules and use GATK or samtools to call variants? But still I don't know how different it will be compared to illumina reads.
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