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We are using the --dbsnp option in HaplotypeCaller. There are several cases where an indel hit against dbsnp appears to not be annotated. For example...
3 33188384 . TA T 455.73 ....
3 33188384 rs57153345 TA T . . OTHERKG;RS=57153345;RSPOS=33188385;SAO=0;SSR=0;U3;VC=DIV;VP=0x050000800001000002000200;WGT=1;dbSNPBuildID=129
Stepping through the code, the variant call alleles do not appear to be normalized resulting in the simple reference field comparison to fail.
I believe the unnormalized variant representation is due to other candidate indels at the locus that wound up being filtered upstream.
Can you confirm that this is a bug, or am I missing somethiing?
If this is a bug, is there a workaround?