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ComparativeGenomicsToolkit / Comparative-Annotation-Toolkit

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HPRC test cases #253

Open diekhans opened 3 years ago

diekhans commented 3 years ago

This is a ticket to capture HPRC cases where it seems like CAT should have annotated a gene, but somehow failed

diekhans commented 3 years ago

FCGR2C

2020/04/13 build FCGR2C/ENSG00000244682.7 is a ploymorphic pseudogene It is not present in NA18906.1 at the h1tg000121l:1,443,947-1,462,880 region, despite having transMap alignments

xuxingyubio commented 1 year ago

With the release of 'A draft human pangenome reference', we find CAT is applied to annotations for various assemblies. Is the input hal file obtained directly from Cactus? What does the config file include? Can you share an example with me?