SHAPEIT5 phasing

Question

[Michal Frenkel]

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?

Answer 1

[bk11]

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

Answer 2

[trausch]

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/

[Michal Frenkel]

It worked! thank you!