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

Badly formed genome unclippedLoc: Contig chr1_KI270766v1_alt given as location, but this contig isn't present in the Fasta sequence dictionary

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    Aaron Seo

    Hello,

    I think I figured out the issue:

    There were "*_alt" chromosomal designations in my interval list (.bed file)--- I removed these, and mutect2 ran successfully. 

     

    Thank you!

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    Gökalp Çelik

    Hi Aaron Seo

    We are glad that you solved the issue. Thank you for sharing it. 

    Regards. 

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