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

(How to) Map and clean up short read sequence data efficiently Follow

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    Dear Team,

    I have a WES illumina data set for variant calling. And both forward and reverse files have adapter read-through at the 3' end as attached fastqc report. In that case, if I do not trim those adapter parts (e.g. using a trimmer like trimmomatic), except run MarkIlluminaAdapters would be enough since this step will mark those parts with XT and later disregard in the alignment. Am I correct??

    I have fastq files(R1 & R2) and what I did was run FastqToSam with RG information to create uBAM -> MarkIlluminaAdapters -> SamToFastq -> BWA mem -> MergeBamAlignment 

    Thank you

    Best Regards



    R1 file

    R2 file 





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