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Intervals and interval lists Follow

11 comments

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    registered_user

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

    <chr>:<start>-<stop>
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    WVNicholson

    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"),

     

    William

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  • Neev Liberman and Carolina Paez: I believe that you can not use this syntax. You can either use multiple -L arguments:

    -L chr1 -L chr2 -L chr3 -L chr4 -L chr5

    or use an interval list/bed file with the chromosomes you are after:

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    Neev Liberman

    How do i include sex chromosomes? Also, can you do an interval as stated above like:

    -L <chr1>-<chr23>
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    Carolina Paez

    This article is pretty informative.

    If I want to do an interval of chromosomes, should I use:

     -L <chr1>-<chr5>

    Any guidance will be appreciated.

     

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    Patrícia H. Brito

    Hi,

    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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    Enrico Cocchi

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

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    pollyshawn

    How to set Chr01 and Chr02?

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    Carolina Paez

    Great to know! Thank you, Dror Kessler (‫דרור קסלר‬‎) for your help.

     

     

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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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    Hee-Bum Yang

    This article was very helpful when I perform 'GenomicsDBimport'.

    However, the working GATK format is actually "<chr>:<start>-<stop>", not "<chr> <start> <stop>" as 'registered_user' said when I run 'GenomicsDBimport'.

    Why don't you update this issue on this article?

    It it not easy to find a solution for the beginner.

     

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