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: https://sourceforge.net/p/samtools/mailman/message/34143978/ and http://seqanswers.com/forums/showthread.php?t=46062)
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