bcftools query: Different samples in XXX

[billzt]

I download the 1000 genome files (VCF format) in ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/supporting/GRCh38_positions/

And try to run:

ls *.vcf.gz >vcf.files
bcftools query -f '%CHROM\t%POS\t%ID\n' -r X:2781454-2781454 -v vcf.files

It complains that:

Different samples in ALL.chr10_GRCh38.genotypes.20170504.vcf.gz and ALL.chr11_GRCh38.genotypes.20170504.vcf.gz

However I checked the samples in ALL.chr10_GRCh38.genotypes.20170504.vcf.gz and ALL.chr11_GRCh38.genotypes.20170504.vcf.gz and comfirm that they are the same.

[billzt]

Well, perhaps I'm misleaded by the document. It seems as if bcftools query can only be used on a single file? #421

[pd3]

This feature should work provided that the -v files have the same samples. This was not working but should be fixed now. Thank you for the bug report.

[letslearnwebdev]

Would you please elaborate what you mean by "provided that the -v files have the same samples"?
I am using latest version (i.e. 1.10.2), -v option with two VCF files from different participants, and both VCF files have .tbi and .csi indexes and still I get the same message: "Different samples in sample1.vcf.gz and sample2.vcf.gz".

Here is the command:

bcftools query -R regions_all.tsv -f'[%CHROM\t%POS\t%REF\t%ALT\t%DP\n]' -v vcfs.txt

[pd3]

The option is meant to help in situations where a big VCF is split into chunks, e.g. by chromosome. If this assumption is not met, just run the command on each VCF individually.