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

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7.8 years ago

human_genomeXXX ▴ 10

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 • 2.0k views

ADD COMMENT • link 7.8 years ago by human_genomeXXX ▴ 10

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What's invalid about the output? Be precise.

ADD REPLY • link 7.8 years ago by WouterDeCoster 47k

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

not clear

ADD REPLY • link 7.8 years ago by Pierre Lindenbaum 164k

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