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

java.lang.IllegalArgumentException: Records contained at least one interval that did not validate against the sequence dictionary.



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    Your bam file and interval list dictionaries don't seem to be compatible. Can you check your bam header with samtools and compare that to interval list header?

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    Pedro Miguel Raposo

    Hi SkyWarrior

    Unfortunately, I abandoned the pipeline involving this step, and started to do my analysis with another approach. Since this post is no longer useful to me, I searched how to delete it but I couldn't find how.

    Sorry for wasting your time.

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