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broadinstitute / GATK-for-Microbes

BSD 3-Clause "New" or "Revised" License
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Generate RTG vcfeval summary.txt file as an output concordance wdl #10

Open bhanugandham opened 3 years ago

bhanugandham commented 3 years ago

Goal: Generate RTG vcfeval summary.txt file as an output concordance wdl in addition to the summary file from GATK Concordance tool.

We are currently only reporting concordance summary using GATK Concordance tool. However GATK Concordance does not normalize variants. RTG vcfeval tool on the other hand does better with comparing similar variants with different representations. The challenge with RTG vcfeval is that it generates concordance for SNVs and INDELS combined.

bhanugandham commented 3 years ago

RTG summary.txt file seems to be saved but not present in output in the ah_shift_bool branch