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Pilon version 1.7
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@w1bw w1bw released this 12 Mar 02:46
· 123 commits to master since this release
v1.7
7aeca2c

This release fixes two VCF-related bugs:

  1. Sometimes equivalent but shifted deletions (think STRs) could be called, one by alignment pileups and one by local reassembly. In some cases, Pilon failed to filter out one of them, leaving overlapping deletion calls in the VCF. These overlapping changes did not make it into the improved FASTA file, it was just an issue when generating the VCF.
  2. In a haploid variant calling run, if the base immediately following an insertion should have been tagged with the Amb (ambiguous) filter, it was not, leaving it looking like a PASSing heterozygous SNP call (which shouldn't happen in a haploid genome!).

Also, this version is built with Scala version 2.10.3.

--bruce, 11 Mar 2014

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