Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
The VCF file generated by GATK HaplotypeCaller does not contain SOR information.
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?