Samtools and Bcftools versions

Hi, I am having trouble with Samtools and Bcftools. I am trying to call SNPs using mpileup and bcftools.

I am using this command: samtools mpileup -q 20 -Q 10 -ugf genome.fa -b list_of_bams.list | bcftools call -vmO z -f GQ -o my_vcf/compressed_vcf.vcf

I am getting this error message.

[vcf.c:759 bcf_hdr_read] invalid BCF2 magic string: only BCFv2.2 is supported.

The mpileup command appears to be working fine (correct output when executed without the pipe to bcftools).

My understanding is that this is because the versions of samtools and bcftools installed on the system (Version: 0.1.19-96b5f2294a and Version: 1.2, respectively), are incompatible with each other, and may need to be updated. (see: and

I am running Ubuntu.

Would it please be possible to update the software versions (if this is the reason behind my problem), or would it be easier to install and run updated versions on my account and use them instead?

Thanks in advance :slightly_smiling_face:


Hi Tris
It looks like you’re using samtools and bcftools from Ubuntu repository. Unfortunately they’re quite old and useless.

We have a GVL image that comes with up-to-date versions preinstalled (“Launch a Genomics Virtual Laboratory server” on

If you’re running regular Ubuntu you have to uninstall existing versions and install new ones from source ( yourself.


Hi Radoslaw,

Thanks for getting back to me - additional problem I have is that launching servers from Warwick is prohibited at the moment - should I just hang tight and try and launch a GVL later?



There is a room for a few more instances at Warwick at the moment so I’ve re-enabled the region. Feel free to launch GVL there


This topic was automatically closed 14 days after the last reply. New replies are no longer allowed.