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

Deep sequencing data is missing variants in M2 called vcf Follow

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    Hi, I will call  vcf  in the  deep seqeuncing data ( 10,000x coverage ) with Mutect2. Should I set --max-reads-per-alignment-start 0  ?


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