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

Intervals and interval lists Follow


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    I can't find anything convincing on how to create a valid Picard interval file although the above information suggests a recipe involving creating the header with "samtools -H" and then adding the required intervals by hand or otherwise.  That may be a dirty hack that could problems in the long run though.  One of the online discussion forums has a thread about this issue and points to a Broad Institute GATK page that no longer exists ("Preparing the essential GATK input files"),



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    Took me a while to figure this out, but the GATK list format is actually:

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    Enrico Cocchi

    How do we download these blacklists that you state you made available?

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    Patrícia H. Brito


    How can I access these WDS interval lists?

    "We make our WGS interval lists available, and the good news is that, as long as you're using the same genome reference build as us, you can use them with your own data even if it comes from somewhere else -- assuming you agree with our decisions about which regions to blacklist!"

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    Aldhair Médico

    Dear GATK developers,
    I'm trying to run Mutect2 for WES cancer data. 
    However, since the Resource bundle only supports h19 seems I cannot proceed.

    I've been looking for some hg38 interval_list file and I found: ''hg38_v0_HybSelOligos_whole_exome_illumina_coding_v1_whole_exome_illumina_coding_v1.Homo_sapiens_assembly38.targets.interval_list''

    However, when I run the GenomicsDBImport I get the error (no matter if I use my own hg38 reference and .dict or the ones from your Resource Bundle):
    ''A USER ERROR has occurred: Badly formed genome unclippedLoc: Contig chr1 given as location, but this contig isn't present in the Fasta sequence dictionary''

    So, my questions are: 
    1. Is there any release date for this hg38 based exome interval file? will it be soon?
    2. Or the file I put is ok and the error is coming from somewhere else?

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    How to set Chr01 and Chr02?

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