I upgraded to GATK 3.5 to use MuTect2 and it works great! However, I'm now using the updated .jar in my germline variant calling pipeline and there's some issues. I only noticed it when I went to run VQSR, and the INDELs went through but not the SNPs. I got an error in the SNP log about the MQ annotation. It seems to be completely absent in the haplotype caller output (the .g.vcf's). I tried forcing it with -A RMSMappingQuality but it did not affect the output. However it works fine if I go back to 3.4
Command Line for 3.4:
java -Xmx4g -jar /REDACTED/tools/gatk_3.4.0/GenomeAnalysisTK.jar -T HaplotypeCaller -R /REDACTED/resources/b37/gatkBundle/human_g1k_v37_decoy.fasta -I /REDACTED/melanoma/bam/recal/PFM-32.ra.rc.bam -L /REDACTED/resources/b37/targetRegions/nexteraRapidCapture_expandedExome/1.bed -ERC GVCF -o /REDACTED/melanoma/variantCall/gatk3.4/gvcf/PFM-32/PFM-32_chr1.g.vcf -A RMSMappingQuality
Command Line for 3.5:
java -Xmx4g -jar /REDACTED/tools/gatk_3.5.0/GenomeAnalysisTK.jar -T HaplotypeCaller -R /REDACTED/resources/b37/gatkBundle/human_g1k_v37_decoy.fasta -I /REDACTED/melanoma/bam/recal/PFM-32.ra.rc.bam -L /REDACTED/resources/b37/targetRegions/nexteraRapidCapture_expandedExome/1.bed -ERC GVCF -o /REDACTED/melanoma/variantCall/gvcf/PFM-32/PFM-32_chr1.g.vcf -A RMSMappingQuality
And here's a single line from the output of each at the same position
3.4:
1 1431520 . C A,<NON_REF> 118.77 . BaseQRankSum=0.452;DP=14;MLEAC=1,0;MLEAF=0.500,0.00;MQ=60.00;MQRankSum=-1.485;ReadPosRankSum=-0.452 GT:AD:GQ:PL:SB 0/1:8,6,0:99:147,0,187,170,205,375:4,4,2,4
3.5:
1 1431520 . C A,<NON_REF> 118.77 . BaseQRankSum=0.710;ClippingRankSum=0.452;DP=14;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.452;RAW_MQ=50400.00;ReadPosRankSum=-1.614 GT:AD:DP:GQ:PL:SB 0/1:8,6,0:14:99:147,0,187,170,205,375:4,4,2,4
I didn't notice anything relevant in the 3.5 release notes except for something about VQSR and MQ jittering which leads me to believe that MQ is indeed a valid annotation still, but how can I get it?
Thanks in advance