Mark

Actually, I had several windows open and post above was meant for PacBio support, which I also had open. That said, I do have a question, relevant here. These large deletions are not being detected by varscan using either mpileup2cns or mpileup2indel though they are present in the bam files and rendered in IGV. Is Varscan capable of detecting deletions (or insertion) of this size when the aligners has accuately mapped them and if so what would the command line be?

I have 2.3 kb amplicons, from several samples, that have be sequenced with PacBio by a third-party and delivered as CCS fastqs. Many of these samples contain reads with large deletions (~1600bp) in their centers and some samples contain only such reads. Note that the samples sent to this third party were run on gels and shown to contain only the 2.3kb amplicon. Though, given the nature of these sample, it is possible that these deletions are real, I think it is more likely they are artefacts of the...

Hello Is it true that only mate-pair reads, not paired end reads, can be used by...

Saw your post and I think we may be having the same problem. See mine at https:/...

Hello I'm trying to call variants on an alignment of pacbio data to a reference thusly:...

unexpected bowtie2 unpaired alignment behavior