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

Data pre-processing for variant discovery Follow

3 comments

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    Robert Bremel

    It would be good to point out that the fastq --> bam needs to include the read group tags because they are needed at the recalibrate base quality scores stage of the process and later

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    Kountay Dwivedi

    Hi,

    I am a Junior Researcher, and I need to familiarise myself with GATK Best Practices. But I cannot find out sample dataset to test Data Pre-processing. Please help me out. Thanks. 

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    yh guo

    Hi,

    I was recently confused about the parameters of sortbam in the call snp flow. At the main steps, you mentioned "SAM/BAM format sorted by coordinate", even in wdl script of "Data Pre-processing", the SAM/BAM file is sorted by "coordinate" (--SORT_ORDER "coordinate"). However, the parameter does not appear as --ASSUME_SORT_ORDER "queryname" until MarkDuplicates. This is very likely to mislead the use of the wrong parameters if the analysis is performed with other software. I hope you can correct it to make it clearer to users. Thank you.

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