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Question: mpileup calling every ALT <X>
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gravatar for rquigl01
2.4 years ago by
rquigl01 • 10
rquigl01 • 10 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 • 1.5k views
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modified 2.4 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.4 years ago by rquigl01 • 10
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gravatar for Jennifer Hillman Jackson
2.4 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link written 2.4 years ago by Jennifer Hillman Jackson ♦ 25k

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 REPLY • link written 2.4 years ago by rquigl01 • 10
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