User: eennadi

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eennadi0
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Posts by eennadi

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(Closed) Help with GATK protocol
... I wish to call variant using the GATK workflow. However, I am having problems 1. Indel re-aligner. I am confused with this step "Restrict realignment to provided intervals". How do I get the GATK intervals I downloaded dbSNP from NCBI database in VCF format but 2. Realigner Target Creator for use ...
deprecated gatk software error tool variant written 3 months ago by eennadi0 • updated 3 months ago by Jennifer Hillman Jackson25k
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How can I index a file with tabix?
... 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: ...
freebayes galaxy gatk vcf variant written 5 months ago by eennadi0 • updated 5 months ago by Jennifer Hillman Jackson25k

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