Hi all,
After sorting my Bam file using Samtools, I tried to use samtools mpileup and bcftools commands for SNP calling. However, I got the following error: [E::cg] unknown type
Does anybody could tell me what should I modify in my command line to avoid this error?
Thanks
Hi Mohamed,
Can you tell us which version of samtools you're using, please? Also, if you could edit your question to include the commands you're running, that would be helpful. Based on similar problems I've read about though, I'd suggest that maybe you're not using the most recent version of samtools. In this case, running your command with the latest version might solve your problem. Alternatively, perhaps you are using the latest version but you're using the -b,v,c or g options? As I understand it, these are now obsolete or have different functions, so could be causing problems.
Take a look at these links for a bit more information:
https://www.biostars.org/p/105431/
https://www.biostars.org/p/145089/
Cheers,
Ian
Hi Ian,
Thank you very much for your reply. I do not think that the problem is linked to the Samtools version since I am using the latest version. Meanwhile, you have reason. The problem could be related to -b,v,c or g options. I'll check!
Many thanks again
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