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

Switching version of gatk during the workflow


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    Gökalp Çelik

    Hi JooYoung Park

    Our team usually does not recommend switching to different versions of GATK for analysis unless it is recommended by us in a documented manner. However you may be able to use GATK 4.2 or later with a CombineGVCFs product or GenomicsDBImport product using 


    parameter to enable genotyping old GVCFs with RAW_MQ and DP tags separated. Though due to unforeseen changes in the code and long forgotten but fixed bugs along the way this combination may still yield problematic results so your mileage may vary. 

    Besides GATK version 3 should also have -L parameter for GenotypeGVCFs therefore you may use 

    -L contig_name

    to run the tool on a single chromosome only. 

    Below is the output of the tool for those parameters. 

    The Genome Analysis Toolkit (GATK) v3.8-1-0-gf15c1c3ef, Compiled 2018/02/19 05:43:50
    Copyright (c) 2010-2016 The Broad Institute
    For support and documentation go to
    [Mon Nov 06 16:42:13 UTC 2023] Executing on Linux 6.5.0-10-generic amd64
    OpenJDK 64-Bit Server VM 1.8.0_111-8u111-b14-2~bpo8+1-b14
    -L,--intervals <intervals>                                                               One or more genomic intervals 
                                                                                              over which to operate
     -XL,--excludeIntervals <excludeIntervals>                                                One or more genomic intervals 
                                                                                              to exclude from processing
     -isr,--interval_set_rule <interval_set_rule>                                             Set merging approach to use 
                                                                                              for combining interval inputs 
     -im,--interval_merging <interval_merging>                                                Interval merging rule for 
                                                                                              abutting intervals (ALL|
     -ip,--interval_padding <interval_padding>                                                Amount of padding (in bp) to 
                                                                                              add to each interval

    I hope this helps. 

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