What parameters to set in SNPEff to improve annotation results from the Pilon VCF input to SNPEff?
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4.9 years ago

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 • 1.5k views
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What's invalid about the output? Be precise.

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

not clear

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