Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

GVCF - Genomic Variant Call Format Follow


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    Hello All,

    I tried to call GTAK 'HaplotypeCaller gvcf mode' and it ran successfully. Output gvcf file showing the following header information

    ##ALT=ID=NON_REF,Description="Represents any possible alternative allele not already represented at this location by REF and ALT"

    I checked with some other gvcf file in online, including GATK example file, and it showing the ALT header as

    ##ALT=ID=NON_REF,Description="Represents any possible alternative allele at this location".

    Please can somebody tell me that is there any mistake in my output gcVF file or is it normal ?

    GTAK command used for Haplotype call** : gatk- HaplotypeCaller --java-options '-Xmx10G' -R
    pdsk_genome.fa -I w_00001.bam -O wgs_00001.g.vcf -ERC GVCF --minimum-mapping-quality=20 --min-base-quality-score=20 --tmp-dir=tmp


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    Jacob Shujui Hsu

    How to determine if there is a missing position? Is this the only case?

    GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0
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    Jeremy Leipzig

    I'd like to see what an unknown (./.) block looks like

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    Hi shameem,


    Did you ever figure it put what is the difference between these two?



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