MPile up Result contains "X" in Alt column

Question

[Bioinformatician_in_trouble]

Hi everyone, I am trying to use mpileup(samtools) for variant calling. In my results which happens to be a VCF file, I get " X" in alt column. The documentation on mpileup says that "In the BCF generated by SAMtools, an non-ref base 'X' represents an base has not been seen from the alignment data. Such a base is necessary to evaluate the probability of missing a non-ref allele due to sampling fluctuation." I do not know how to fix this error. Can someone please help. Your help would be much appreciated. Thanks :) PS: I am using mpile up in galaxy and not on command line.

[Devon Ryan]

Is this on usegalaxy.org or a different site? At the command line, at the command line, we'd use bcftools call, but I don't know if this available on your Galaxy instance.

[Bioinformatician_in_trouble]

Thank you both of you for your reply. @ Devon Ryan: It is a local instance of galaxy. And My output from mpileup is a VCF file, so I am not sure how useful will Bcftools will be. @ Berge2015 :Thank you,I did see these posts.But again,it was on command line. And I am using the web version of galaxy.

[Devon Ryan]

bcftools call accepts gVCF input, which is what you have.

Answer 1

[berge2015]

Google is your friend. A couple of posts to get you started: 1) Samtools Mpileup With Refrence Addition 2) Mpileup BCF/VCF output without non-ref base 'X'? Good luck!