Entering edit mode
9.2 years ago
stefano.iantorno
▴
70
Hello
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
Thanks,
- Stefano
Which version of bcftools are you using?
Edit: BTW, that error normally only happens when it attempts to read BCF in from a pipe and that's in an older format.
Version 0.1.19-44428cd
You are correct, after updating to the latest version it works!
Could you give us the output of:
I'm showing the first two variants for brevity. This is a non-human organism so disregard unusual chrom names. The first is a phased SNP the second is unphased