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

variant calling: dict and indexing


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    Louis Bergelson

    Hi Nagarajan Raju,

    You do need to sort the bam file and indexing it after sorting.  If you haven't done the other preprocessing steps we recommend you might want to do those as well (MarkDuplicates, BQSR).

    There is an article describing our recommended steps.  The sorting happens usually as part of the MarkDuplicates step using the tool called SortSam.

    The simplest example would be something like this:

    gatk SortSam INPUT unsorted.bam OUTPUT sorted.bam SORT_ORDER coordinate


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