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

Physical Phasing oh alleles


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    Gökalp Çelik

    Hi Shanmugavadivel Subramaniam

    Numeric values in GT fields represent the allele present in the genotype. 0 represents REF alelle whereas 1 represents the first ALT allele, 2 represents the secont ALT allele and so on. If you have only a single number present at both sides of the phase or genotype sign then that site is homozygous. Otherwise different numbers mean heterozygosity if the sample is diploid. So in short 1|1 is HOM_ALT and 0|1 or 1|0 is HET. 

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