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how to extract LOF variants from vcf file?

hi all

i have a vcf file resulted from whole genome sequencing project and now i want to extract heterozygote and homozygote loss function (LOF) non synonymous SNPs. how can i do it?

thanks in advance

variants vcf loss function variants
• 2,915 views • link
written by reza reza

See the Variant Effect Predictor from Ensemble. An awesome tool, but a bit bulky and tricky at times. Did cost me a lot of nerves but I think well worth it. Here are the docs, come back if you have questions.

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written by ATpoint ATpoint

i annotated vcf file using snpeff but i do not now how find LOFs

• 1 views • link
written by reza reza

i found that i must add -lof option to my command to vcf annotation as following:

java -jar snpEff.jar eff -v -lof BB_12 WC247_final_snps.vcf > WC247_final_snps_lof.vcf

but there is no LOF tags in INFO fields. what part of my work is fault? it is worth to mention that building of database for annotation done by myself in snpEff.

• 0 views • link
written by reza reza

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