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

GetPileupSummaries output all 0


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    Gökalp Çelik

    Hi Estel

    Can you try running these commands with the latest GATK version 4.4 and with Java 17. Java 11 has never been officially supported. We recommend Java 1.8 (8) for versions and below and Java 17 is the standard version for GATK 

    Also we have a few more comments about why this could be happening. It seems that only a small number of reads are getting filtered and the whole process seems to be ending very quickly. This tells us that either your bam files are pretty much empty and there are no usable reads inside due to bad MQ or else, OR those sites that you are using to collect pileup summaries may not be matching to where your reads actually are. Can you check on these possibilities before escalating this issue? 



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