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

Allele Depth (AD) is lower than expected Follow


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    Shashank Katiyar

    Thanks, this is a well explained article about a much needed missing information. I wonder if is there any parameter to change the 'difference between the Phred scaled likelihoods' from .2 to the desired number?

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    It'll be helpful to report read coverage after filtering for each sample in the output of GenotypeGVCFs

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