Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.
I am trying to understand the definition of NTLEN in the pindel vcf output. The header says that it is: "Number of bases inserted in place of deleted code". It makes sense for RPL variants where a chunk of bases are deleted and a sequence is inserted.
However, in duplications based on the figure 2e: http://gmt.genome.wustl.edu/packages/pindel/new-development.png in Pindel's user manual, it looks like its just an inserted sequence between reference and duplicated sequence. There isnt anything deleted here. So, this definition seems applicable only to RPL variants and not when we observe non template sequence for duplicated events. I just wanted to clarify so that I am not missing anything.
Hi,
I am trying to understand the definition of NTLEN in the pindel vcf output. The header says that it is: "Number of bases inserted in place of deleted code". It makes sense for RPL variants where a chunk of bases are deleted and a sequence is inserted. However, in duplications based on the figure 2e: http://gmt.genome.wustl.edu/packages/pindel/new-development.png in Pindel's user manual, it looks like its just an inserted sequence between reference and duplicated sequence. There isnt anything deleted here. So, this definition seems applicable only to RPL variants and not when we observe non template sequence for duplicated events. I just wanted to clarify so that I am not missing anything.
Thank you. Ashini