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Question: HOW TO REALIGN INDELS
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gravatar for julieta
9 weeks ago by
julieta • 10
julieta • 10 wrote:

Hello. I want to know what is the best tool to realign indels using galaxy. Thank you.
galaxy variant indel realign bam • 100 views
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modified 9 weeks ago by Jennifer Hillman Jackson ♦ 25k • written 9 weeks ago by julieta • 10
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gravatar for Jennifer Hillman Jackson
9 weeks ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

If you use Freebayes to do the variant calling, realignment is performed by that tool during execution (a distinct realign step is not needed).

If using a different caller, try BamLeftAlign.

Please see the Galaxy variant analysis tutorials for the full details and example protocols: https://galaxyproject.org/learn/

Note: Avoid using GATK in Galaxy as all of those tool wrappers have been deprecated. New versions are under development but not quite available yet.

Thanks! Jen, Galaxy team
ADD COMMENT • link modified 9 weeks ago • written 9 weeks ago by Jennifer Hillman Jackson ♦ 25k
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