I am using GATK HaplotypeCaller to call variation with the following command:
java -Xmx20g -jar GenomeAnalysisTK.jar -l INFO -R hg19.fa -T HaplotypeCaller -nct 16 -I D-2.realigned.recal.bam -I D-3.realigned.recal.bam -I D-4.realigned.recal.bam --dbsnp hg19_GATK_snp137.vcf -o D-2_D-3_D-4.raw.vcf -A StrandOddsRatio -A AlleleBalance -A BaseCounts -A StrandBiasBySample -A FisherStrand
However, there is a problem in the VCF file generated by this command. The SOR information in the header definition line did not exist in the mutation list.
##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias">
chr1 13116 rs201725126 T G 94.57 . AC=1;AF=0.250;AN=4;BaseQRankSum=1.754;DB;DP=7;FS=0.000;MLEAC=1;MLEAF=0.250;MQ=29.47;MQ0=0;MQRankSum=-1.754;QD=23.64;ReadPosRankSum=-0.550 GT:AD:GQ:PL:SB 0/0:3,0:9:0,9,191:0,0,0,0 0/1:1,3:44:123,0,44:0,0,0,0 ./.
I have tried VariantAnnotator but still got the same problem.
Could you please tell me where the problem exist and how to solve it?
Thanks !