Question: Extracting Variants from large set of variants
0
gravatar for bioinfo355
19 months ago by
bioinfo3550
Pakistan
bioinfo3550 wrote:

I have a vcf file of whole genome of human and it has millions of variants. Is there any way to extract my own variants of interest from these millions of variants? And even good if extracting variants on the basis of their 'rs IDs'

wgs data vcf variant calling • 438 views
ADD COMMENTlink modified 19 months ago by ammar.husami0 • written 19 months ago by bioinfo3550

from bcftools manual expressions section https://samtools.github.io/bcftools/bcftools.html:

ID=@file .. selects lines with ID present in the file

ID!=@~/file .. skip lines with ID present in the ~/file

you can use either bcftools view or filter

ADD REPLYlink modified 19 months ago • written 19 months ago by cpad011212k
0
gravatar for Pierre Lindenbaum
19 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum126k wrote:

GATK SelectVariants https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_tools_walkers_variantutils_SelectVariants.php

And even good if extracting variants on the basis of their 'rs IDs'

--keepIDs / -IDs

List of variant IDs to select
If a file containing a list of IDs is provided to this argument, the tool will only select variants whose ID field is present in this list of IDs. The matching is done by exact string matching. The expected file format is simply plain text with one ID per line.
ADD COMMENTlink written 19 months ago by Pierre Lindenbaum126k
0
gravatar for ammar.husami
19 months ago by
ammar.husami0 wrote:

in VCF, the variants are mapped to the genome reference, in some cases there will be rs ID's in the VCF but it's best to extract based on the coordinates.

ADD COMMENTlink written 19 months ago by ammar.husami0
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