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

Checking of GATK script


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    Gökalp Çelik

    Hi RN Sarma

    There are multiple issues with this commandline based on your purpose. 

    1- HaplotypeCaller does not have a parameter named and therefore using it will throw an error message.


    If you wish to filter INDELS and just get SNPs then you can use 

    gatk SelectVariants --select-type SNP

    to get SNP calls only. 

    2- The below parameter will not return only biallelic sites but it will limit the number of called alternate alleles per loci to 1 and will drop all other alleles if there are more present. If you wish to get only biallelic sites then you may drop this parameter as well and just call variants and perform variant selection using the tool that I mentioned above to get what you exactly need. 

    --max-alternate-alleles 1

    I hope this helps. 


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