Missing ReadPosRankSum, MQRankSum and BaseQRankSum Scores in VCF

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Hamza Umut Karakurt

• December 14, 2020 08:33

If you are seeing an error, please provide(REQUIRED) :
a) GATK version used: 4.0
b) Exact command used: gatk BaseRecalibrator -I SRR303332.marked.bam  -R hg19.fa --known-sites dbsnp138_r_hg19.vcf.gz -O SRR30_recal_data.table 

gatk ApplyBQSR -R hg19.fa -I SRR30.marked.bam --bqsr-recal-file SRR30_recal_data.table -O SRR30.marked.recal.bam 

Hello everyone,

I am new at GATK and I am working on one of my old collegue's analyses. I am sorry if my questions are too basic.

Apparently I noticed something; final VCF file of an WGS experiment has missing values of ReadPosRankSum, MQRankSum and BaseQRankSum scores. Missing values are not "NA", they have a point character "." instead. Other columns do not have any missing values.

Is any of the values are related with homozygotic/heterozygotic? Should I remove the variants with these values? As I know there is not any filtering applied to that VCF due to our project.

Thank you in advance.

 

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  Genevieve Brandt (she/her)

  • December 18, 2020 17:25

  Hi Hamza Umut Karakurt, could you clarify this information:

  • How was the VCF file obtained? Was it with GATK?
  • Is there an issue with BQSR, since you supplied the commands above?
  • Which specific version of GATK4 are you using?
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