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 yields none mutation records

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    Genevieve Brandt (she/her)

    Hi zhexin liu,

    Thanks for writing into the forum so that we can help you solve this issue! To me, it looks like your bam file is empty. There are no reads filtered in any of the read filters ("0 total reads filtered") and also none of the lines in the GVCF have any read support. 

    You'll want to look at your process of downloading the bam and make sure you downloaded it properly.

    Best,

    Genevieve

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