Question: mpileup calling every ALT <X>
gravatar for rquigl01
18 months ago by
rquigl0110 wrote:

Im using the mpileup application on galaxy and every base is being called with the ALT <x>. It has 110,000,000 lines as well which seems to be too much. I'm just trying to call SNPs and INDELS. Here is a screenshot. Does anybody know what I am doing wrong?

galaxy mpileup • 685 views
ADD COMMENTlink modified 18 months ago by Jennifer Hillman Jackson23k • written 18 months ago by rquigl0110
gravatar for Jennifer Hillman Jackson
18 months ago by
United States
Jennifer Hillman Jackson23k wrote:


This prior post at has help for the same issue: See Devon's reply (currently the second answer).

In Galaxy: When using MPilieup, output BCF (instead of VCF) then convert to VCF excluding non-ATGC bases with the tool bcftools view.

Hopefully this helps! Jen, Galaxy team

ADD COMMENTlink written 18 months ago by Jennifer Hillman Jackson23k

on bcftools view, there is an option to skip sites where the REF field is not A/C/G/T, but my problem is in the ALT column. What option on bcftools are you referring to?

ADD REPLYlink written 18 months ago by rquigl0110
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