Ideas to filter known SNPs

[dawe]

Hi all, I have a VCF file which contains a raw list of mutations/snps for my study. I would like to exclude known SNPs from dbSNP131/hg19 (which I also have in VCF format).
I was thinking about BEDTools, something like

intersectBed -a MyList.vcf -b hg19.snp131.vcf.gz -v > specific.vcf

but AFAIK this only exclude those variations that happen at the same position. That means that if I have a novel variation at the same position, that would be excluded too.
Does anybody have an idea/processing pipeline to deal with this? I was looking at vcftools but couldn't find anything helpful
d

[dawe]

Nevermind, I've realized that I can feed GATK Unified Genotyper with known SNPs and filter them out in a second step
d

[bioinfosm]

that sounds like a useful thing to do. but looking at the GATK Unified genotyper, it seems more of a multiple samples tool than one to exclude known dbSNP variants, etc.
Did I miss something here

[dawe]

Originally Posted by bioinfosm

that sounds like a useful thing to do. but looking at the GATK Unified genotyper, it seems more of a multiple samples tool than one to exclude known dbSNP variants, etc.
Did I miss something here

It is.
I could use it to identify variants *and* to filter out known ones.
d

[JohnK]

I have a script you can mod to remove SNPs in dbSNP. Just holla' if you need/want it. Just tweak it to perform on a vcf of bed file.

[bioinfosm]

@dawe,

It would be great if you could share the gatk functionality to do so. Better use use a standard and available tool than re-invent

[Michael.James.Clark]

@bioinfosm: Just use the -D parameter with a dbSNP .rod file. See the GATK wiki for more about how that works (it's part of their default variant calling flow).

Originally Posted by dawe

Nevermind, I've realized that I can feed GATK Unified Genotyper with known SNPs and filter them out in a second step
d

I know it's an old thread, but I just started using VCFtools and found how it can do this.

Use the --exclude parameter and feed it a list of all the SNP IDs you used to mark your VCF when you ran it through the Unified Genotyper.

Since you used GATK, you can make that list from the SNP .rod pretty easily:

awk '{print $5}' dbsnp_130.rod > dbsnp_130_snpIDs.txt

Then run vcftools:

vcftools --exclude dbsnp_130_snpIDs.txt --vcf <in.vcf> --out <out.prefix>

If you want to make a new VCF that contains only the novels, just add on the --recode option.

Not bad, and doesn't take too long to run.

Of course, you can pretty easily grep out the lines that have an ID to accomplish the same thing almost instantaneously, but still.

[moty]

Originally Posted by dawe

Nevermind, I've realized that I can feed GATK Unified Genotyper with known SNPs and filter them out in a second step
d

Can you please elaborate?
I could not find how to perform this second step.
I am trying to filter out some known SNPs from dbSNP135. while I have both my variation file and the dbSNP file (both .vcf) I can't find a way to exclude the latter from the former.

[Petr]

Hi,

vcf-isec is exactly what you are looking for: intersections, complements etc. on VCF and TAB delimited files.

[aforntacc]

Hello guys,
please i cant see SNP ID in my data the ID column is represented with dot (.)
and now i am trying to filter out snp from the indel. samtools was used for the calling.
how can i do this.
thanks

chr1 8686 . T C 38.7 MfGtMis;AltSup AC1=12;AF1=1;DP4=0,0,1,5;DP=6;FQ=-28.6;MQ=16;MfGt=1/1;MinDP=0;NeqMfGt=0 GT:PL : DP:SP:GQ 1/1:0,0,0:0:0:5 1/1:40,9,0:3:0:13 1/1:0,0,0:0:0:5 1/1:0,0,0:0:0:5 1/1:34,9,0:3:0:13 1/1:0,0,0:0:0:5
chr1 10802 . T C,A 999 MfGtMis AC1=12;AF1=1;DP4=0,0,5,17;DP=284;FQ=-38.1;MQ=33;MfGt=1/1;MinDP=2;NeqMfGt=0 GT:PL : DP:SP:GQ 1/1:91,15,0,91,15,91:5:0:31 1/1:131,18,0,131,18,131:6:0:34 1/1:53,6,0,53,6,53:2:0:22 1/1:44,6,0,44,6,44:2:0:22 1/1:67,9,0,67,9,67:3:0:25 1/1:70,21,12,55,0,52:4:0:25
chr1 10815 . A G 999 MfGtMis AC1=12;AF1=1;DP4=0,0,26,11;DP=315;FQ=-42.4;MQ=38;MfGt=1/1;MinDP=3;NeqMfGt=0 GT:PL : DP:SP:GQ 1/1:109,18,0:6:0:38 1/1:188,39,0:13:0:59 1/1:120,15,0:5:0:35 1/1:69,9,0:3:0:29 1/1:43,9,0:3:0:29 1/1:89,21,0:7:0:41
chr1 10836 . C A 999 MfGtMis AC1=11;AF1=0.9836;DP4=2,0,32,5;DP=313;FQ=-28.4;MQ=33;MfGt=1/1;MinDP=1;NeqMfGt=0;PV4=1,4.1e-10,1,1 GT:PL : DP:SP:GQ 1/1:49,12,0:4:0:21 1/1:15,3,0:1:0:12 1/1:90,23,0:11:0:32 1/1:83,0,8:7:0:3 1/1:130,39,0:13:0:48 1/1:56,9,0:3:0:18