Please help with Eagle

Question

[seta]

Hi all,

I got a vcf file of a single chromosome containing about 1121 samples (derived from whole genome sequencing) for phasing by Eagle2, but it returned the below error:

[E: vcf_parse_format] Number of columns at chr9:133255595 does not match the number of samples (1120 vs 1121)
Read M= 0 variants
Filling in genetic map coordinates using reference file:

genetic_map_hg38_withX.txt

Segmentation fault

Regarding the vcf file, given the header, the bcftools concat command used on this vcf file.

Could you please kindly help me to solve the issue?

Thanks in advance

[Bioinformatics_NewComer]

If you're working with CHR9, it could be good to work with genetic map for CHR9 only.