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's -bamout created BAM-file not showing reads even with --force-active and --output-mode EMIT_ALL_ACTIVE_SITES

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    Genevieve Brandt (she/her)

    Hi Vee Koo,

    The bamout only shows sites where variants are present. If you want to see all your reads, you should stick to the input bam.

    Let me know if you have further questions.

    Best,

    Genevieve

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    Vee Koo

    Okay, is it then safe to assume that those empty spaces contain only reads that are similar to the reference genome?

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    Genevieve Brandt (she/her)

    I think for what you are trying to do, I wouldn't recommend using the bamout. It's only meant for specific troubleshooting but not further analysis.

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