The VCF file generated by GATK HaplotypeCaller does not contain SOR information.

YiJiang

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 !

Sheila

@YiJiang
Hi,

I used the latest version. It looks like SOR was introduced in 3.3 as a standard annotation. http://gatkforums.broadinstitute.org/discussion/4739/release-notes-for-gatk-version-3-3

-Sheila

Sheila

@YiJiang
Hi,

I hope this article helps you: http://gatkforums.broadinstitute.org/discussion/6022/i-do-not-get-the-annotations-i-specified-in-haplotype-caller?new=1

-Sheila

YiJiang

Thank you very much. I tried "-G Standard" but still got the same problem. Is there any problem in my command? Here is my 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 -G Standard -A DepthPerSampleHC -A ClippingRankSumTest -A AlleleBalance -A BaseCounts -A StrandBiasBySample -A FisherStrand -A StrandOddsRatio

@Sheila said:
YiJiang
Hi,

I hope this article helps you: http://gatkforums.broadinstitute.org/discussion/6022/i-do-not-get-the-annotations-i-specified-in-haplotype-caller?new=1

-Sheila

Sheila

@YiJiang
Hi,

I just tried the same command as you, and I get SOR in my VCF. Can you tell me which version of GATK you are using? Did you include the bam file as input to Variant Annotator?

Thanks,
Sheila

YiJiang

@Sheila
Thank you very much.
The version I am using is GenomeAnalysisTK-3.1-1. Is this version suitable? May I ask what version you are using?
I did not include the bam file as input to Variant Annotator. I am using only VCF file as input. Did this influence the result?
Here is the command of running Variant Annotator:
java -Xmx18g -jar GenomeAnalysisTK.jar -T VariantAnnotator -R hg19.fa -V D-2_D-3_D-4.snp.vcf --dbsnp hg19_GATK_snp137.vcf.gz -o D-2_D-3_D-4.snp.VariantAnnotator.vcf -A StrandOddsRatio -nt 20 -L Exome.bed --disable_auto_index_creation_and_locking_when_reading_rods
Thanks,
Yi Jiang

YiJiang
Hi,

I just tried the same command as you, and I get SOR in my VCF. Can you tell me which version of GATK you are using? Did you include the bam file as input to Variant Annotator?

Thanks,
Sheila

Sheila

@YiJiang
Hi,

I used the latest version. It looks like SOR was introduced in 3.3 as a standard annotation. http://gatkforums.broadinstitute.org/discussion/4739/release-notes-for-gatk-version-3-3

-Sheila

YiJiang

@Sheila
Thanks you very much. I downloaded a latest version and it works.

YiJiang
Hi,

I used the latest version. It looks like SOR was introduced in 3.3 as a standard annotation. http://gatkforums.broadinstitute.org/discussion/4739/release-notes-for-gatk-version-3-3

-Sheila