Hello everybody, I ran across an issue while trying to phase my genomic data with Sanger Phasing (Eagle). For some reason the phased file I received from sanger (called all.vcf.gz) only includes some of the genetic variants/snps (no snps from the 6th chromosome and onwards are included in the file); while the file I uploaded for phasing (vcf.gz formatted) includes variants from all 24 chromosomes (including X and Y).

I didn't receive any error notifications from sanger during the process.

Does anybody knows what can be the issue?

Thank you!