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

HaplotypeCaller does not recognize the RefSeqfile

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    Newcomer

    Thanks!

    When I fixed f.dict and .fai file , it worked fine.

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    Bhanu Gandham

    Hi Newcomer

     

    Your input fasta file is Bos_taurus.ARS-UCD1.2.dna.toplevel.fasta. GATK is looking for Bos_taurus.ARS-UCD1.2.dna.toplevel.fasta.fai and not Bos_taurus.ARS-UCD1.2.dna.toplevel.fa.fai. Take a look at the suffixes. Once you fix that it should be good to go.

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