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Posts by eennadi
... 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 ...
... 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: ...
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