how to extract LOF variants from vcf file?

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5.8 years ago

reza ▴ 300

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 • 2.2k views

ADD COMMENT • link 5.8 years ago by reza ▴ 300

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search this site for SNPEff and / or VEP

ADD REPLY • link 5.8 years ago by Pierre Lindenbaum 161k

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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.

ADD REPLY • link 5.8 years ago by ATpoint 82k

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

ADD REPLY • link 5.8 years ago by reza ▴ 300

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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.

ADD REPLY • link 5.8 years ago by reza ▴ 300

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