Bcftools
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3 months ago

Hello ! I am trying to use bcftools to filter my vcf files. Honestly I don't really understand the syntax rules and the usage of commands. I have looked through the manual, it's still confusing to me. I wanted to ask if it is possible to filter my file so that samples included have filter PASS and their funcrefgene column has value "exonic ". Could you please help?

bcftools vcf • 334 views
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"bcftools" is not a correct title. Edit your title please.

I have looked through the manual , still confusing to me

show us what you tried. And we don't know what is the "funcrefgene" column.

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I'm assuming OP is referring to the ANNOVAR INFO/Func.refGene field.

kamila, please look at the -i (include) option and sample expressions in the bcftools view subcommand.

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