Question: MPileup output errror ALT <X> QUAL 0
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gravatar for edouglasrobertson
4 months ago by
edouglasrobertson0 wrote:

When using MPileup I received an error in that all the output was for chr10 (even when my file only contained info for chr20), the ALT position was always X, and the quality score was 0. Therefore for some reason the variant calling failed but I don't know why. Can anyone help?

mpileup • 163 views
ADD COMMENTlink modified 4 months ago by Jennifer Hillman Jackson22k • written 4 months ago by edouglasrobertson0

There might be a reference genome mismatch problem. Double check that the same genome was used for the mapping step as was assigned for the option "Using reference genome" on the Mpileup tool form. If using a Custom reference genome, ensure that it was first run through the tool NormalizeFasta with the option to wrap at 80 bases and clip the title line at the first whitespace (or is in that format already).

If you cannot determine the problem and are either working at http://usegalaxy.org or can reproduce the problem there, an email with a shared history link can be sent to galaxy-bugs@lists.galaxyproject.org. Please also include a link to this post.

Thanks, Jen, Galaxy team

ADD REPLYlink written 4 months ago by Jennifer Hillman Jackson22k

I've sent a link to my history. Its not a custom reference so I don't see what the problem is.

ADD REPLYlink written 4 months ago by edouglasrobertson0
0
gravatar for Jennifer Hillman Jackson
4 months ago by
United States
Jennifer Hillman Jackson22k wrote:

Hello,

The input fastq sequence quality is very, very low. It may not be usable. Run FastQC to review.

The quality impacts mapping (very few sequences map at all) plus all downstream steps. GATK tools failing is a known - these are deprecated and not recommended. Alternative variant detection methods are covered in the tutorials.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 4 months ago by Jennifer Hillman Jackson22k
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