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Illumina / GTCtoVCF

Script to convert GTC/BPM files to VCF
Apache License 2.0
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Additional B allele frequency and log R ratio (BAF and LRR) Format fields #20

Closed brianhill11 closed 5 years ago

brianhill11 commented 6 years ago

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. ".").

jjzieve commented 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.