Are the variant calls in IGSR phased?

You can tell when a VCF file contains a phased genotype as the delimiter used in the GT field is a pipe symbol | e.g

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  HG00096
10   60523  rs148087467    T     G       100     PASS    AC=0;AF=0.01;AFR_AF=0.06;AMR_AF=0.0028;AN=2; GT:GL 0|0:-0.19,-0.46,-2.28

The VCF files produced by the final phase of the 1000 Genomes Project (phase 3) are phased. They can be found in the final release directory from the project and in the directory supporting the final publications.

Some other studies have also produced phased versions of their calls. These include the analysis of high-coverage data across 3,202 samples on GRCh38 completed by NYGC. Multiple sets of VCFs are available, including phased VCFs, linked to from the page for that collection.

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