I am trying to run bcftools view -p to filter only the SNPs that have phased genotypes, but I keep getting either empty files or the following error message:
[bcf_sync] incorrect number of fields (0 != 5) at 0:0
Immediately following the VCF file header. Do I need to convert the vcf back to bcf?
Please help, the command I'm running is:
bcftools view input.vcf -p