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

Is there a GATK tool for quantifying a particular base?


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    Gökalp Çelik

    Hi M Carta

    Welcome to bioinformatics. 

    In order to collect such data you can force calls of those alleles of interest by using Mutect2 and the parameter


    Output VCF files will contain allelic fractions of those sites in the FORMAT fields as well as number of reads supporting the reference and alternate alleles. 

    If you wish to obtain pileups for those positions of your interest you can use 

    gatk Pileup 


    samtools mpileup

    and you may combine that output with an auxiliary tool such as 

    java -jar varscan.jar readcounts

    to obtain a tabular list of reads supporting each nucleotide per position. As a warning the latter 2 are not directly within our reach to provide support and your mileage may vary. 

    I hope these would help your endeavors. 


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