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HaplotypeCaller lost 80% variants in a sample
We have several close-related samples each contain 3 million variants relative to the reference genome (both UG and HC give this results for most samples), while HC only give less than 1 million for a few samples. I searched the forum and did some test, and failed to figure out why this happen.
Here goes some detailed descriptions:
I tested two samples, those two look very similar, and the mapping results both seem proper with good mapping quality (>20)
HC gives proper varaint results and output bam file for sample1:
However, the sample2 gives the similar mapping results, but HC did not give any variants, the output bam file contain no sequence, after adding "--disableOptimizations --forceActive" options, the output bam file contain one sequence without any variants
The strangest thing is when I tried joint-calling of two samples, those variants called in sample1 also get disappeared, and the output bam file is sample as the sample2
Those reads were generated from Hiseq4000 platform, most base qualities are also high (Illumina seems changed the highest quality value to 42, I'm not sure whether this could affect, however other samples seem proper ...).
Thank you very much in advance!