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vcf file processing

I have a vcf file, have run SnpEff for annotation. I need to group these snps based on their belong genes. such as x, y and z snps belong to gene w, for all gene.

snp next-gen gene
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updated by GenoMax GenoMax • written by neeraj4biotech • neeraj4biotech

Are you trying to extract them into separate files per gene or are you trying to run a burden test or something sophisticated?

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written by Vivek Vivek

Thanks Vivek for quick response. Have vcf file and bed/gff file as input file. Actually I want separate files per gene.

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written by neeraj4biotech • neeraj4biotech

There are more elegant solutions if you can do some scripting but here's a crude workflow:

If you have one line per gene in the bed file, you can initially split the BED file into one file per gene like this:

split -l 1 Genes.bed Genes-

Depending on the number of genes, you might produce a lot of files here.

Rename to bed extension

for file in `ls Genes-*`;do mv $file $file.bed;done

Then use Tabix to split your VCF

for bed in `ls Genes-*.bed`;do tabix variants.vcf -h -B $bed > variants-${bed}.vcf;done
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written by Vivek Vivek

It always helps if you can post some example data. Use datamash to group by gene and collapse all SNPs.

output:

$ datamash -H -g 1 collapse 2 < snps.txt 
GroupBy(gene)   collapse(snp)
x   a,b,c
y   d,e
z   f,g,h

input:

$ cat snps.txt 
gene    snp
x   a
x   b
x   c
y   d
y   e
z   f
z   g
z   h

Install datamash either from here or from distro repos (for debian based; sudo apt install datamash -y; for conda, conda install datamash -y).

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written by cpad0112 cpad0112

Neeraj, can you post few lines of the data? I know it should be a standard vcf, still it helps !

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written by lakhujanivijay lakhujanivijay

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