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

1

Entering edit mode

7.2 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 • 1.9k views

ADD COMMENT • link 7.2 years ago by human_genomeXXX ▴ 10

1

Entering edit mode

What's invalid about the output? Be precise.

ADD REPLY • link 7.2 years ago by WouterDeCoster 47k

1

Entering edit mode

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

not clear

ADD REPLY • link 7.2 years ago by Pierre Lindenbaum 161k

Login before adding your answer.