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

BedToIntervalList Error

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    David Benjamin

    Vincent Appiah $dict and $bedFile are probably inconsistent.  It looks like your BED file contains an interval on chr1 that starts at 249104618, while your sequence dictionary says chr1 ends at 248956422, which is the case for hg38.  In hg19 chr1's length is 249250621 and you should have no problems.

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    Vincent Appiah

    Hi David,

    You are right. I was able to run using hg19. Thanks for the info

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