What software can better substitute SNPEff for the tuberculosis whole genome annotation?
What software can better substitute SNPEff for the tuberculosis whole genome annotation?
annotation
whole genome
tuberculosis
• 3,529 views
•
link
written
by
human_genomeXXX
1
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Using SnpEff on Galaxy
written by pmenon0998 1I have been trying to use SNPeff on Galaxy to annotate a vcf file. I am working with the genome of Mycobacterium tuberculosis, and hence …
-
what software is a proper one for the GWAS of the tuberculosis?
written by bioinform 3what software is adequate for the GWAS of the tuberculosis? i have a 1000 of VCF and a matrix of phenotypic features, what modern software …
-
Need help to choose 2-3 genome annotation software from the list at https://omictools.com/genome-a…
written by human_genomeXXX 1Need help to choose 2-3 genome annotation software from the list at https://omictools.com/genome-annotation-category Input will be a VCF files generated from the Pilon, BBMap, GATK …
-
How to download tuberculosis reference using the last version of SNPEff?
written by human_genomeXXX 1How to download tuberculosis reference using the last version of SNPEff? I have tried java -jar snpEff.jar download -v m_tuberculosis.reference
-
Is it correct to try to use the newest ClinEff annotation software for the tuberculosis genome?
written by human_genomeXXX 1Is it correct to try to use the newest ClinEff annotation software for the tuberculosis genome?
-
How to reduce annotation errors using SNPEff on BBMap`s and Pilon`s VCFs?
written by human_genomeXXX 1How to reduce annotation errors using SNPEff on BBMap and Pilon VCFs? I get "chromosome not found" error in Tuberculosis genome data processing experiments and …
-
What parameters to set in SNPEff to improve annotation results from the Pilon VCF input to SNPEff?
written by human_genomeXXX 1I run the code line: java -Xmx10G -jar snpEff.jar -c snpEff.config -s SNPEffOutputStats.html -v -no-downstream -no-upstream m_tuberculosis_H37Rv pilon_output.pilon.vcf > SNPEffSampleGenome_merge.var.ann.vcf And it produces results, but …
-
How to download and set up a Tuberculosis H37rv whole genome in SNPEff software?
written by human_genomeXXX 1How to download and set up a Tuberculosis H37rv genome in SNPEff software? I have tried and it can`t read the reference .gb genome. How …
-
What is the fastest whole genome aligner available in Galaxy cloud software?
written by genomicswolf 2What is the fastest whole genome aligner available in Galaxy cloud software? Also need to choose the most precise and accurate variant callers appropriate for …
-
How to process/visualize snp.matrix WGS data?
written by fashiondesignrussian 6I have snp.matrix and phenotype.csv data. How to process them correctly? Are there any books/chapters/papers/tutorials and software? My task is to visualize and analyse the …
Maybe VEP? http://www.ensembl.org/info/docs/tools/vep/index.html
If I'm not mistaken SNPEff is (only) for variant annotation. What type of genome annotation would you like to do? Annotation is a quite broad term...
I have a Pilon, VarScan and BBMap different .snp and .vcf outputs. Need to annotate them (separately) to see a human readable report with gene names and statistical situation printed out. Thank you.