Phasing a Single-Sample VCF File on GRCh38

[lucianhu]

Dear shapeit5 Team,

I have created a VCF file using the nf-core sarek / DeepVariant pipeline, which contains data for only one individual. I'm seeking guidance on how to perform phasing for this single-sample VCF file based on GRCh38.

I've explored options SHAPEIT5 with 1KG_GRCh38 but unfortunately, they do not seem to work for my scenario.

SHAPEIT5_phase_common -I vcf_by_chrom_chr1.vcf.gz -M chr1.b38.gmap -R chr1 -H ALL.chr1.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf.gz -O vcf_by_chrom_chr1.phase.vcf.gz -T 10 --progress

[SHAPEIT5] phase_common (jointly phase multiple common markers)
  * Author        : Olivier DELANEAU, University of Lausanne
  * Contact       : olivier.delaneau@gmail.com
  * Version       : 5.1.1 / commit = 5.1.1 / release = 2023-05-16
  * Run date      : 26/12/2023 - 17:47:56

Files:
  * Input         : [vcf_by_chrom_chr1.vcf.gz]
  * Reference     : [ALL.chr1.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf.gz]
  * Genetic Map   : [chr1.b38.gmap]
  * Output        : [vcf_by_chrom_chr1.phase.vcf.gz]
  * Output format : [bcf]

Parameters:
  * Seed    : 15052011
  * Threads : 10 threads
  * MCMC    : 15 iterations [5b + 1p + 1b + 1p + 1b + 1p + 5m]
  * PBWT    : [window = 4cM / depth = auto / modulo = auto / mac = 5 / missing = 0.1]
  * HMM     : [window = 4cM / Ne = 15000 / Recombination rates given by genetic map]

Reading genotype data:
  * VCF/BCF scanning done (0.01s)
      + Variants [#sites=0 / region=chr1]
         - 2754 sites removed in main panel [not in reference panel]
         - 4 sites removed in main panel [multi-allelic]

ERROR: No variants to be phased!

my VCF has also AC and AN tags.

I appreciate any assistance or recommendations you can provide.

Happy New Year and thank you,

Nhu