Annotating the multi sample vcf file

Question

[Peerzada]

Hello all ,

I annotated the multi sample VCF file using ensemble-VEP command line. I got all the mutations in the vcf file but the information regarding which sample has which mutation is not there . How can I get the information that which mutation is in which sample.

Thank you

[Pierre Lindenbaum]

look at the genotypes FORMAT/GT ....

[Peerzada]

There is not any column naming Format .It only contain positioin and the nucletide change as well as some other information like amino acid changes.

[barslmn]

What is the format of your output? Or better what was your command for calling VEP?

[Peerzada]

Format of output was text file and I used ensemple-Vep for annotation with the following command.

vep --cache -i my_protein.vcf --filter Consequence is missense_variant -o my_protein_filter_vep.txt

[Pierre Lindenbaum]

output as VCF to keep the genotypes.

[Peerzada]

I kept the output as vcf ,yet the output do not have sample information.

[Peerzada]

Also I have this variant data from 1000g .

[Pierre Lindenbaum]

if the input protein.vcf don't have any genotype, you cannot get the affected samples -- quod erat demonstrandum .

[Peerzada]

My input vcf file have genotypes as well as sample names of about 2500 individulas.IT is mentioned there.

[Pierre Lindenbaum]

please, show us the output of:

bcftools query -l my_protein.vcf | head -n1

and

vep --cache -i my_protein.vcf --filter "is missense_variant" --vcf -o my_protein_filter_vep.vcf

bcftools query -l my_protein_filter_vep.vcf | head -n 1

[Peerzada]

bcftools query -l my_protein.vcf | head -n1

HG00096

bcftools query -l my_protein_filter_vep.vcf | head -n1
HG00096

But when I am changing the output to vcf format , I cannot know how to analyze that as there is no clear visualization of the samples there.I tried to analyze it as excel file but there is lot of mess created.

[Pierre Lindenbaum]

., I cannot know how to analyze that as there is no clear visualization of the samples there.

so THIS is your real problem. You have to learn to analyze/filter a VCF file. Have a look at snpSift, etc... search biostars.org .

I tried to analyze it as excel file but there is lot of mess created.

[Peerzada]

Thank you Sir .I will try to .

[Peerzada]

I tried using snpSift and Jvarkit but I am not able to get the command that will simplify my multi sample annotated vcf file to get the sample information of each variant . I am very new to this . Kindly provide the solution for the same.