Bcftools

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12 months ago

kamila.temirkhanova • 0

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 • 504 views

ADD COMMENT • link updated 12 months ago by Ram 44k • written 12 months ago by kamila.temirkhanova • 0

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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.

ADD REPLY • link updated 12 months ago by Ram 44k • written 12 months ago by Pierre Lindenbaum 164k

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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.

ADD REPLY • link 12 months ago by Ram 44k

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