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

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    Genevieve Brandt (she/her)

    Thank you for your post, Jakub Savara! I want to let you know we have received your question. We'll get back to you if we have any updates or follow up questions. 

    Please see our Support Policy for more details about how we prioritize responding to questions. 

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    Jakub Savara

    Thank you very much!

    I just wanted to be sure, since e.g. bedtools requires name sorted bam. However, I tried SamToFastq (GATK) for both coordinate and name sorted bam (paired) and the read count in fastq is exactly the same. Also after alignment the result is identical (using samtools flagstats).

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