It worked! thank you!
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Michal Frenkel •
SHAPEIT5 phasing
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?
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Michal Frenkel •
2 answers
Here is the link 1000 Genomes on GRCh38- https://www.internationalgenome.org/data-portal/data-collection/grch38
Here is the reference panel for hg38: https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/working/20220422_3202_phased_SNV_INDEL_SV/
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