Question: how to extract LOF variants from vcf file?
gravatar for reza
21 months ago by
reza220 wrote:

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

ADD COMMENTlink written 21 months ago by reza220

search this site for SNPEff and / or VEP

ADD REPLYlink written 21 months ago by Pierre Lindenbaum127k

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 REPLYlink written 21 months ago by ATpoint32k

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

ADD REPLYlink written 21 months ago by reza220

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 REPLYlink written 20 months ago by reza220
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