ERROR: Population based phasing for less than 20 individuals

[yaowei2010]

I got this error with my input vcf, is it not recommended to pre-phasing one sample by shapeit4?

The input VCF is generated by the variant calling in WGS or WES platform, and it is not under pre-phasing.

If we want to do this, where can find the reference panel for variant files from WGS or WES data?
Thanks.

The input have been indexed by bcftools.

ps: I have not error when compiling shapeit4 with library HTSlib and BOOST.

shapeit4.2 --input K2841.vcf --map chr1.b37.gmap.gz --output phased.chr.vcf --region 1 --thread 4

---

`SHAPEIT

• Author : Olivier DELANEAU, University of Lausanne
• Contact : [email protected]
• Version : 4.2.2
• Run date : 09/06/2022 - 16:47:01

Files:

• Input VCF : [K2841.vcf]
• Genetic Map : [chr1.b37.gmap.gz]
• Output VCF : [phased.chr.vcf]

Parameters:

• Seed : 15052011
• Threads : 4 threads
• MCMC : 15 iterations [5b + 1p + 1b + 1p + 1b + 1p + 5m]
• PBWT : Depth of PBWT neighbours to condition on: 4
• PBWT : Store indexes at variants [MAC>=2 / MDR<=0.5 / Dist=0.02 cM]
• HMM : K is variable / min W is 2.50cM / Ne is 15000
• HMM : Recombination rates given by genetic map
• HMM : AVX2 optimization active

Initialization:

• VCF/BCF scanning ...
  ERROR: Population based phasing for less than 20 individuals is not permitted, use a reference panel to solve this issue!`

[odelaneau]

Hi,

1000 Genomes project is a good starting point.

Best

O