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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    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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    registered_user

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

    <chr>:<start>-<stop>
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