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

Mutect2 guide for multiple lanes?

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    Daniel von Rhein

    Simply merge your fastq files into one big fastq-file.

    In Linux, this could look like this

    zcat DS-bkm-085-N_L00{1,2,3,4,5,6,7}_RG.fastq | gzip > DS-bkm-085-N_merged_RG.fastq

     

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    David Benjamin

    vctrymao Currently you have different sample names for each lane, which is activating multisample mode in recent releases of Mutect2 (since 4.1 or maybe 4.1.1, I think).  You should give every tumor read group the same SM tag.

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