Fail to subset VCF file by chromosomes

[MaayanYoles]

Hi,

My data consists of about 4000 subjects with a vcf file for each and the aim is to merge them all together and split by chromosomes.
I used "bcftools merge -m none -Oz -o output_file input_files" to merge them,
and "bcftools view -r chr_number input_path -Oz -o output_path" to split.

The merge went OK with no errors and a huge file made. When merging, still no raised errors, but it works only for the first 3 chromosomes. for the rest, a small file is made with the sample names and nothing more.

Would love some advice, since this makes no sense. worth noting - I checked the personal files and for sure they have all chromosomes in them.

Thank you so much,
Best,
Maayan

[pd3]

What version of bcftools do you have? If it is the latest, would you be able to isolate the problem and create a minimal test case for us to reproduce? This would be a serious bug indeed.

[MaayanYoles]

Fist of all, thank you so mach for the quick response!

I use bcftools 1.9, installed from bioconda about 2 weeks ago.

Maayan

[pd3]

Uh, try with the latest version then and see if the problem persists
http://samtools.github.io/bcftools/howtos/install.html