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
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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