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

gatk workflow on non human genomes

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    Gökalp Çelik

    Hi Naama Yefet

    Short answer you cannot but you can adapt. 

    Depending on the way you design your experiment you can pretty much use similar preprocessing workflows to get your aligned reads ready for variant calling. You may need to consider omitting BQSR step as you may not have enough resource to pick gold standard variants. If all your samples are sequenced latest sequencing technologies such as NovaSeq, you may consider BQSR as an optional step and omit since new sequencers have better calibrated base calling metrics, optics and chemistry. 

    For variant calling there are 2 options ahead.

    1- If you are working with pooled samples and just interested in getting allele fractions in your samples you may continue with Mutect2 Microbial/mitochondria mode. 

    2- If you are dealing with individually sequenced samples but interested in performing joint genotyping, then HaplotypeCaller and GenotypeGVCFs is your friend. Beware that you need to set the ploidy properly when calling and genotyping samples and  also keep in mind that haploid mode can still capture potentially heterozygous looking calls that may be handled at your discretion. Also VQSR may not be an immediate option for you unless you have a set of gold standard variants at hand. You may want to resort to hard filtering options and fiddle with those parameters that we recommended for human samples. 

    I hope this helps.

    Regards. 

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    Naama Yefet

    Hi Gökalp Çelik , thank you for your comment. i would like to further emphasize my question. I am working on my thesis of WGS analysis on thousands of samples of candida auris individually seqenced genomes to find variations associated with violence and drug resistance. the analysis includes preprocessing and variant calling. i would like to run the analysis on terra cloud and explore the option of using preconfigured workflows. however, i am new to the cloud and not fully familiar with it's functions. my question is: 1. is there an option to use gatk preconfigured workflow designed for human genome and modify it in the cloud although some required inputs of the workflow dont exist in candida auris genome, and if so how can it be done.  2. if modifying preconfigured workflow designed for human genome is problematic on the cloud, is there a possibility of creating a new workflow fitting my data from scrath in terra cloud. in addition, i would like to hear your input, what do you consider is the best approach to run my analysis?

    thank you 

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    Gökalp Çelik

    Hi again. 

    To get support on how to adjust your workflows using the preconfigured ones on Terra you need to use the terra community forum as they will be the first hand support for this. We may not be able to help directly to configure your terra environment for your project. This support requires you to understand the workflow language basics, using your own repository to keep your workflow and locating your resource files for reference genome etc.

    For more help on Terra

    https://support.terra.bio/hc/en-us/community/topics 

    I hope this helps.

    Regards. 

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