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Question: How can I index a file with tabix?
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gravatar for eennadi
10 months ago by
eennadi • 0
eennadi • 0 wrote:

I used freeBayes to call variants. Running it on the program I wanted to use it for it returned this [W::vcf_parse] Contig 'cneoH99_Chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'cneoH99_Chr9' is not defined in the header. (Quick workaround: index the file with taxi.)

Please can someone help me with how to index a file with tabix in galaxy?
variant vcf gatk galaxy freebayes • 328 views
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modified 10 months ago by Jennifer Hillman Jackson ♦ 25k • written 10 months ago by eennadi • 0
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gravatar for Jennifer Hillman Jackson
10 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

GATK tools (all) have been deprecated in Galaxy. I can see that you have found the alternative tools instead now and those jobs are successful.

My guess is that there was a genome mismatch or sorting problems with the data. Indexing will not correct those sorts of issues. Still, the utility tabix is in the Tool Shed http://usegalaxy.org/toolshed, could be used in a local/cloud Galaxy, but it may or may not work as it was wrapped some time ago. It is not on the public servers.

Examples of how to perform Variant analysis are in the Galaxy tutorials: https://galaxyproject.org/learn/

Support FAQs: https://galaxyproject.org/support/

Thanks! Jen, Galaxy team
ADD COMMENT • link written 10 months ago by Jennifer Hillman Jackson ♦ 25k
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