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.
Hi,
I got a question referring to "sample name + 6 numbers" pattern and the number for AD tag when looking through the output files from pindel. Could you please help me out?
By the way, just want to clear up that the larger one of these 2 numbers will be used as the first number in AD tag when converting pindel result to vcf file, right?
Screenshot below is the text I read, as you can see, both "read depth" and "reference coverage" are used in describing the first 2 numbers, so which one is correct, the ref OR ref + alt
Hi, I got a question referring to "sample name + 6 numbers" pattern and the number for AD tag when looking through the output files from pindel. Could you please help me out?
First, the 6 numbers following sample name, I have already read the explanations from https://github.com/genome/pindel/commit/b706fba61c64a11fb1d3716d501fd2f4d8992e29. Still confused about the first 2 numbers, are they the depth (ref + alt) or only the ref count?
By the way, just want to clear up that the larger one of these 2 numbers will be used as the first number in AD tag when converting pindel result to vcf file, right?
Screenshot below is the text I read, as you can see, both "read depth" and "reference coverage" are used in describing the first 2 numbers, so which one is correct, the ref OR ref + alt
Thanks, Nan