Question: MPile up Result contains "X" in Alt column
gravatar for Bioinformatician_in_trouble
3.4 years ago by

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.

mpileup samtools galaxy • 973 views
ADD COMMENTlink modified 3.3 years ago • written 3.4 years ago by Bioinformatician_in_trouble10

Is this on 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.

ADD REPLYlink written 3.4 years ago by Devon Ryan94k

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.

ADD REPLYlink written 3.3 years ago by Bioinformatician_in_trouble10

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

ADD REPLYlink written 3.3 years ago by Devon Ryan94k
gravatar for berge2015
3.4 years ago by
berge201590 wrote:

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!

ADD COMMENTlink written 3.4 years ago by berge201590
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