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How to extract all columns of CSQ using split-vep plugin of bcftools?

I have a vcf file containing CSQ column which has 350 parameters. How can extract all of them as table using bcftools +split-vep

plugin samtools bcftools vcf split-vep
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updated by hello_bioinf • hello_bioinf • written by DareDevil DareDevil

extract all of them as table using

is this plugin able to convert vcf to a tabular format ?

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written by Pierre Lindenbaum Pierre Lindenbaum

1 answer 

bcftools +split-vep -f '%CHROM\t%POS\t%REF\t%ALT\t%CSQ\n' -d -A tab input.vcf

And if you need headers:

echo -e "CHROM\tPOS\tREF\tALT\t$(bcftools +split-vep -l input.vcf | cut -f 2 | tr '\n' '\t' | sed 's/\t$//')" > output.tsv
bcftools +split-vep -f '%CHROM\t%POS\t%REF\t%ALT\t%CSQ\n' -d -A tab input.vcf >> output.tsv
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written by David Parry • David Parry

Hi David,

Love the code, thanks! Do you know if its possible to get the ensembl vep headers onto the output? Thanks! Amy

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written by hello_bioinf • hello_bioinf

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