Closed brianhill11 closed 5 years ago
@brianhill11 See merging of #41 it should have all the updates from this PR. I just rebased it from develop with some tweaks and added in support for indels. If there are any problems feel free to open another issue.
Added support for (optionally) generating B allele frequency (BAF) and log R ratio (LRR) format fields. The command line argument for adding these fields is
--include-attributes BAF LRR
. Multiple records for a single site are merged by taking the median value, disregarding any NaN values. The B allele frequency is merged by first normalizing by strand, and then by normalizing to the reference allele. For both fields, if a tri-allelic site (or more) is found, a missing value is returned (i.e. ".").