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'm interested in detecting internal tandem repeats in FLT3 with Pindel. Is there a way to determine (or even estimate) the variant allele frequency? I see an AD for the alt allele, but the ref portion of AD is always zero in my results, and the RD field is never used.
This is my VCF result for a 300bp TD from the Horizon HD829 reference.
I'm interested in detecting internal tandem repeats in FLT3 with Pindel. Is there a way to determine (or even estimate) the variant allele frequency? I see an AD for the alt allele, but the ref portion of AD is always zero in my results, and the RD field is never used.
This is my VCF result for a 300bp TD from the Horizon HD829 reference.
This is the relevant pindel output: