bcftools consensus genome, get not all chromosomes sequences!

[CrawlingSponge]

Dear pd,
Thank you for the software. When I use bcftools "consnensus genome" to get a pesudogenome with 20 chromosome numbers (genome size: about 2.5G), I only got three chromosomes and the left ones could not generate. I have double-checked the reference genome and its index, and the vcf includes all variations information along all 20 chromosomes.

So why I just got the former tree complete sequences, that is curious.

I tried to generate the left chromosomes sequences one by one using bcftools consensus commond, and there are no variants applied. Is there any parameters I need to add to generate the sequences?

PS: the vcftools version is V1.11

many thanks
best regards

[pd3]

Thanks for the issue, however, it does not give enough information, not sure how to help! One common problem is the chromosome naming (chr1 vs 1), which needs to be the same in both the fasta and the VCF file. Another thing to check is to update to the latest version, we are now at 1.19. The simplest way to use the program is described here http://samtools.github.io/bcftools/howtos/consensus-sequence.html.

If none of the above helps, a small test case to reproduce the problem will be required.