Hi there - any help appreciated here, I'm a relative newbie to NGS evaluation.
I'd like to be able to detect low level deletions of 15bp (or more) in an amplicon-enrichment based assay. We are using Novoalign for alignment, followed by samtools and varscan for variant ID. This all works find up to ~6bp.
I have tried pindel etc. with limited success. As the deletions we are looking for are relatively recurrent, I was thinking of trying a synthetic reference approach. I'm unclear how I can integrate this alignment strategy with our alternative standard reference alignment.
I'd prefer to create a single fasta file as a reference, but for all of the short synthetic deletion sequences I append (one per record), I'd like to preserve their original chromosomal position etc.
Am I dreaming?
Any help or other recommendations much appreciated!
I'd like to be able to detect low level deletions of 15bp (or more) in an amplicon-enrichment based assay. We are using Novoalign for alignment, followed by samtools and varscan for variant ID. This all works find up to ~6bp.
I have tried pindel etc. with limited success. As the deletions we are looking for are relatively recurrent, I was thinking of trying a synthetic reference approach. I'm unclear how I can integrate this alignment strategy with our alternative standard reference alignment.
I'd prefer to create a single fasta file as a reference, but for all of the short synthetic deletion sequences I append (one per record), I'd like to preserve their original chromosomal position etc.
Am I dreaming?
Any help or other recommendations much appreciated!
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