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MQ annotation missing

Hi all,
I have a minor concern.

After using CombineVariants tools to combine variants from GATK and Samtools, MQ annotation is missing for some of the variants specifically for variants which are present in both GATK and Samtools. Below is an example:

$grep "16203159" VCF/GatkSNP.vcf
chr8    16203159    .   G   T   4609.77 .   AC=1;AF=0.500;AN=2;BaseQRankSum=-7.105;ClippingRankSum=0.652;DP=333;     
GT:AD:DP:GQ:PL  0/1:163,170:333:99:4638,0,4651

$ grep "16203159" VCF/SamSNP.vcf
chr8    16203159    .   G   T   225 .   DP=346;VDB=4.969420e-01;RPB=-1.470555e+00;AF1=0.5;AC1=1;DP4=82,84,81,92;  
MQ=58;FQ=225;PV4=0.66,6.2e-09,1,1   GT:PL:GQ    0/1:255,0,255:99

MQ annotation is present in both the VCF files. But after combining MQ is missing as shown below:

$ grep "16203159" TMP_files/SNP_INDEL.vcf
chr8    16203159    .   G   T   4609.77 .   AC=1;AC1=1;AF=0.500;AF1=0.5;AN=2;BaseQRankSum=-7.105;  
GT:AD:DP:GQ:PL    0/1:163,170:333:99:4638,0,4651

Variants which are present in only of the VCF files do have MQ annotation after using CombineVariants. This happens only for variants which are present in both VCF files. Could you help to get MQ annotations in this case?

Here is the command used:

java -jar GenomeAnalysisTK.jar -T CombineVariants -R ref.fa --variant:GatkSNP GatkSNP.vcf --variant:GatkINDEl GatkINDEL.vcf  
--variant:SamSNP SamSNP.vcf --variant:SamINDEL SamINDEL.vcf -o SNP_INDEL.vcf -genotypeMergeOptions PRIORITIZE -priority    
GatkSNP,GatkINDEL,SamSNP,SamINDEL --filteredrecordsmergetype KEEP_UNCONDITIONAL


  • meharmehar Member ✭✭

    I checked the documentation for CombineVariants tool to find if, by adding optional flags or optional parameters to the command line might solve the problem. Unfortunately, it seems there isn't any such fix. Any suggestions to fix this would be highly valuable.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hey @mehar, can you please not post the same question in two different places? It clutters up the forum. We have been slow to answer questions this week because we are very busy with a GATK workshop, but that does not mean we are forgetting you.

    I will check but I think this is just a limitation of the tool that it is unable to combine certain annotations.

  • meharmehar Member ✭✭

    Hi Geraldine,

    Sorry for the inconvenience. Will not post duplicate queries in the future.

    I hope there will be a fix soon to combine MQ annotations and awaiting to hear about it asap.

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