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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 fails with Exit code 3, but no further information is given

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    Bhanu Gandham

    Looks like HaplotypeCaller is unable to read the input file. Try to run `samtools view -H <inputbam>` and see if that works. If that doesn't work either then it is not a GATK issue and you need to check why the input file is unavailable. 

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    Bhanu Gandham

    Another thing to try is validate your input BAM files with ValidateSamFile 

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    Louisa Normington

    I tried the Picard tool ValidateSamFile. I learned that I had missing read groups so then I ran AddOrReplaceReadGroups. Following that, HaplotypeCaller still didn't work, but this time it told me why, which was that my bam was not indexed, so I ran the suggested code, samtools index. Finally I ran my original command, and it worked. 

    Thanks!

    I find the read group concept confusing. Could you explain it?

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