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SOR annotation related error from VariantRecalibrator

analyst123analyst123 Boston, MAMember

I am getting this error from variant recalibrator:

ERROR MESSAGE: Bad input: Values for SOR annotation not detected for ANY training variant in the input callset. VariantAnnotator may be used to add these annotations

Does this mean I have to bring these in from external resources --- dbSNP? I thought haplotypecaller should bring these tags.
This is what the format haplotypeCaller has produced. There is no SOR annotation. I am working with a single whole genome.

1 14590 . G A 67.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.282;ClippingRankSum=-0.592;DP=13;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=25.74;MQ0=0;MQRankSum=-1.268;QD=5.21;ReadPosRankSum=-1.268 GT:AD:DP:GQ:PL 0/1:10,3:13:96:96,0,411

Best Answer


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