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HaplotyeCaller - non-variant block records in gVCF

fiapintofiapinto PortugalMember
edited February 2016 in Ask the GATK team


I have generated a gVCF for an exome (with non-variant block records) from a BAM file belonging to the 1000Genomes data.
I am using GATK tools version 3.5-0-g36282e4 and I have run the HaplotypeCaller as follows:

time java -jar $gatk_dir/GenomeAnalysisTK.jar \
-T HaplotypeCaller \
-R $reference \
-I $bamfile \
-ploidy 2 \
-stand_call_conf 20 \
-stand_emit_conf 10 \
-o output.g.vcf.gz

Within the purpose of the analysis I am performing, from this gVCF I need to be able to know whether the positions are no-called, homozygous reference, variant sites or if the positions were not targeted in the exome sequencing.

However, with the gVCF file I obtained I am not able to do it because there are only variant site records or non-variant block records where the GT tag is always "0/0".

So I have few questions regarding the non-variant block records:

  1. Why the output file does not contain any no-call ("./.") record?

  2. Shouldn't regions where there are no reads have the tag GT equal to "./." instead of "0/0"?

  3. How can regions without reads (not targeted) be distinguished from regions with reads that were not called?

  4. When looking at the bam file with IGV, non-variant blocks displayed in gVCF contain regions with reads. What is the explanation for such behaviour?

Thank you for your attention,


Best Answer


  • SheilaSheila Broad InstituteMember, Broadie ✭✭✭✭✭

    @fiapinto @Redmar_van_den_Berg

    @Redmar_van_den_Berg Thanks for your fantastic answer! You are right about everything :smile:

    Sofia, I just want to add that if you run GenotypeGVCFs on your GVCFs, you will find the sites that don't have reads or have GQ = 0, will change to no-calls.


  • sangusangu Member

    I get GT:DP ./.:0 for one block of non-variants in gvcf. However, there is enough number of reads for this block. I have another block of non-variants showing GT:DP 0/0:6. But the number of reads for both the blocks is almost similar and I am not getting how these two blocks are differentiated when they have the same number of reads of each position.

    Thank you
  • bshifawbshifaw Member, Broadie, Moderator admin


    Hi ,

    The GATK support team is focused on resolving questions about GATK tool-specific errors and abnormal results from the tools. For all other questions, such as this one, we are building a backlog to work through when we have the capacity. Please continue to post your questions because we will be mining them for improvements to documentation, resources, and tools. We cannot guarantee a reply, however, we ask other community members to help out if you know the answer.For context, see this [announcement](https://software.broadinstitute.org/gatk/blog?id=24419 “announcement”) and check out our [support policy](https://gatkforums.broadinstitute.org/gatk/discussion/24417/what-types-of-questions-will-the-gatk-frontline-team-answer/p1?new=1 “support policy”).

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