Question

How to sort vcf file

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3.7 years ago

shubhamkumbhar420 ▴ 40

Here is a screenshot of my VCF and I want to extract info from an extra column put in each value in a separate column like a standard VCF file!

Thanks in advance!

vcf • 3.5k views

ADD COMMENT • link 3.7 years ago by shubhamkumbhar420 ▴ 40

score 2 · Answer 1 · 2021-03-24

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3.7 years ago

Pierre Lindenbaum 164k

the correct answer would be

bcftools sort your.vcf

but your image shows that it is not a VCF file. The last VCF header should be #CHROM POS ID REF ALT QUAL FILTER INFO... so It's something else... with a VCF header (##).

and the usual associated image:

enter image description here

ADD COMMENT • link 3.7 years ago by Pierre Lindenbaum 164k

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yeah! The VCF file is annotated with 1)snpEff and 2)VEP (variant effect predictor). Now I want to separate the fields. !!!

ADD REPLY • link 3.7 years ago by shubhamkumbhar420 ▴ 40

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Now I want to separate the fields. !!!

? that's not sorting a vcf

ADD REPLY • link 3.7 years ago by Pierre Lindenbaum 164k

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I mean extract the fields. and it's not a proper VCF cause this is generated by VEP (ensemble).

ADD REPLY • link 3.7 years ago by shubhamkumbhar420 ▴ 40