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Alternatively, direct upload your vcf to MegaQuery of VarioWatch (http://genepipe.ncgm.sinica.edu.tw/v...n.do?mega=true) should receive your results online in real time.
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You might also want to try www.gene-talk.de . It is an wiki-like expert platform for filtering and annotating sequence variants. The automatic annotation is based on annovar. For the interpreation of unkown variants other expert users might assist you,...
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Originally posted by ulz_peter View Posttry annovar:
http://www.openbioinformatics.org/annovar/
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Originally posted by ulz_peter View Posttry annovar:
http://www.openbioinformatics.org/annovar/
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Originally posted by genomicist View PostMaybe, try this one:
ftp://gatk-ftp:[email protected]/refGene/
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Annotating VCF files
Can anybody tell me how to annotate vcf files for hg19 aligned file? I tried GATK, vcftools and vcfCodingSnps.
GATK - I couldn't find their refGene file in their ftp server
ftp://gatk-ftp:[email protected]
vcftools: I am having a hard time running it - it gives me "tabix" error
vcfCodingSnps: I was not able to compile on my mac - OS X 10.6, 64 bit
It will be great if anybody can give me a complied code for this architecture.
Thanks.Tags: None
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The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...-
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