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

Seeking Clarification on RNA-seq Variant Calling Pipeline

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    Gökalp Çelik

    Hi Laura Rey Vargas

    Exome sequencing and transcriptome sequencing have quite different fundamentals in terms of data quality, handling and variant metrics. We recommend against using any DNA sequencing workflow to be applied onto variant calling from RNA-seq data as is. 

    We do have a wdl in github  that contains all the steps that are in our current practice. 

    https://github.com/gatk-workflows/gatk4-rnaseq-germline-snps-indels/blob/master/gatk4-rna-best-practices.wdl 

    For the variant filtering part, due to lack of extensive data to train specifically for RNASeq variant calling we recommend single sample hard filtering with thresholds given in the wdl. 

    I hope this helps. 

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