cc175bad40
Dangling head merging (like with tails) in now enabled by default. The --recoverDanglingHeads argument is now deprecated so that users know not to use it anymore. We now also allow the user to set the minimum branch length for merging. This will be different for exomes and RNA (see below). The other changes in the code itself: 1. We no longer allow an arbitrarily large number of mismatches in the dangling head for merging 2. The max number of mismatches allowed in a dangling head is proportional to the kmer size There will be a difference in the RNA calling pipeline. Instead of invoking '--recoverDanglingHeads' the user will instead want to use '--minDanglingBranchLength 0'. Below are the knowledgebase results of the master branch vs. this one. For NA12878 DNA Exome: master SNPS TRUE_POSITIVE 36722 master SNPS CALLED_NOT_IN_DB_AT_ALL 2699 master SNPS REASONABLE_FILTERS_WOULD_FILTER_FP_SITE 292 master SNPS FALSE_POSITIVE_SITE_IS_FP 70 branch SNPS TRUE_POSITIVE 36867 branch SNPS CALLED_NOT_IN_DB_AT_ALL 2952 branch SNPS REASONABLE_FILTERS_WOULD_FILTER_FP_SITE 387 branch SNPS FALSE_POSITIVE_SITE_IS_FP 94 As I discussed with Ryan in person, there are a good number of FPs that are called in the new code, but they nearly all have bad strand bias and should be easily filtered by VQSR. Note that there is no change for indels. For NA12878 RNA from Ami: master SNPS TRUE_POSITIVE 11055 master SNPS CALLED_NOT_IN_DB_AT_ALL 831 master SNPS REASONABLE_FILTERS_WOULD_FILTER_FP_SITE 44 master SNPS FALSE_POSITIVE_SITE_IS_FP 96 branch SNPS TRUE_POSITIVE 11113 branch SNPS CALLED_NOT_IN_DB_AT_ALL 874 branch SNPS REASONABLE_FILTERS_WOULD_FILTER_FP_SITE 47 branch SNPS FALSE_POSITIVE_SITE_IS_FP 92 Again, there's basically no change for indels. |
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