This is a test version of Biostars. For the public version, visit https://www.biostars.org.
What parameters to set in SNPEff to improve annotation results from the Pilon VCF input to SNPEff?

I 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 it can`t see many chromosomes and output is not valid.

What parameters of SNPEff are adequate for running tuberculosis whole genome annotation for the input Pilon`s VCF?

snpeff annotation pilon vcf
• 2,383 views • link
written by human_genomeXXX • human_genomeXXX

What's invalid about the output? Be precise.

• 0 views • link
written by WouterDeCoster WouterDeCoster

And it produces results, but it can`t see many chromosomes and output is not valid.

not clear

• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

0 answers

No answers yet.

Log in to answer this question.

More posts like this