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

GenotypeGVCF not getting all samples

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    SkyWarrior

    Hi Joseph Thorpe

    Since you import your samples in batches of 50 it seems that during the 3rd cycle there is a sample with a problematic index or malformed gvcf file therefore importing crashes after successive 2 cycles and genotyping results with only 100 samples in it. Can you check 3rd batch of 50 gvcf files and their index files for validity?

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