Question: mpileup calling every ALT <X>
0
gravatar for rquigl01
2.1 years ago by
rquigl0110
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. https://gyazo.com/f70ca31ebd7d47421b4e702ae3cb91f3 Does anybody know what I am doing wrong?

galaxy mpileup • 1.1k views
ADD COMMENTlink modified 2.1 years ago by Jennifer Hillman Jackson25k • written 2.1 years ago by rquigl0110
1
gravatar for Jennifer Hillman Jackson
2.1 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

This prior post at Biostars.org has help for the same issue: https://www.biostars.org/p/161981/. 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 2.1 years ago by Jennifer Hillman Jackson25k

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 2.1 years ago by rquigl0110
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