Hello, I'm running into that widespread bug, in which real variant are not called by HaplotypeCaller. There are 10 variants clearly and easily visible to the eye, when viewing the BAM file. However, the whole region with these 10 variants (about 105 bases) is eliminated from the BAMOUT, and thus these are not called. I'm just focusing on this region as a test to troubleshoot this problem, but I expect this to have other occurrences in other regions of the genome.
I tried various tricks :
--force-active, --adaptive-pruning, --linked-de-bruijn-graph, --recover-all-dangling-branches, etc. But no success.
I run HaplotypeCaller on just that region of 105 bases, and they do show on this short bamout alignment and the variants are called. When I rerun the HaplotypeCaller on just this chromosome, same problem, they are not called.
Any suggestions to circumvent this problem?
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