Variable region not considered active region by HaplotypeCaller

Follow

Veronica

• July 15, 2020 22:19

Hello,

I am using GATK v4.0.1.1, and I ran HaplotypeCaller in two libraries of the same sample. Although a given region is similarly variable in both libraries, GATK has only called variants in one of them. This occurs in multiple regions of the genome.

I am attaching an IGV screenshot with an example of this situation.

The command I used was:

gatk HaplotypeCaller -R reference.fasta -I strain.mkd.bam -O strain.vcf -ploidy 2 --genotyping-mode DISCOVERY --standard-min-confidence-threshold-for-calling 30 -bamout strain.GATK.bam

 

Can you please help me understanding what is going on?

 

Thanks in advance.

 

Best,

Verónica

0

• 

  Genevieve Brandt (she/her)

  • July 16, 2020 18:09

  Hi Veronica, could you update your GATK version? We have made a lot of changes to this tool since 4.0.1.1 and you might find much better results with an update.

  0

  Comment actions Permalink

Please sign in to leave a comment.