SHAPEIT5 phasing
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9 months ago

I have a vcf containing data from one family (of 9 individuals, 2 parents and 7 children). When I try to phase the vcf with SHAPEIT5 I get the error:

ERROR: Less than 50 samples is not enough to get reliable phasing, consider using a reference panel to increase sample size

I intend to download a reference panel from the 1000 Genomes Project (phase3) on NCBI. However, I noticed that it is based on the hg19 coordinates. Is there a readily available reference panel aligned with the hg38 coordinates?

SHAPEIT VCF SHAPEIT5 • 955 views
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9 months ago
bk11 ★ 3.0k

Here is the link 1000 Genomes on GRCh38- https://www.internationalgenome.org/data-portal/data-collection/grch38

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It worked! thank you!

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