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Vcf Snps And Indels Mouse Genomes

Hi,

I am using SNPs and INDELs data from the mouse genomes project and the data seem to have conflicting information. I mean, seems they report a SNP in a deleted position.

Thus my question,

Is it possible that there are SNPs at positions that are marked as deletions?

As an example, according to mgp.v3.indels.rsIDdbSNPv137.vcf CASTEiJ is homozygous for the deletion starting at position chr19:3372820, listed below (between **):

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  CASTEiJ
19      3372820 .       TCATATGCACCCTCACCTCACACACCC     T       191.83  PASS    AC1=1;AC=12;AF1=1;AN=12;DP4=1,0,46,40;DP=204;INDEL;MDV=99;MQ=27;MSD=20;PV0=1;PV1=1;PV2=0.0096;PV3=1;PV4=1,1,0.0096,1;QD=0.0088;SB=0.5625;VDB=0.0404;CSQ=ENSMUST00000025835:ENSMUSG00000024900:intron_variant,feature_truncation:Allele,T:Gene,Cpt1a  GT:GQ:DP:SP:PL:FI  **1/1:99:10:0:183,30,0:1**

At the same time, according to mgp.v3.snps.rsIDdbSNPv137.vcf CASTEiJ is homozygous for a SNP at position chr19:3372824 (between **)
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  CASTEiJ
19      3372824 rs264849569     A       G       199.78  PASS    AC1=0;AC=12;AF1=0;AN=36;DP4=299,271,52,63;DP=782;MDV=99;MQ=54;MSD=21;PV0=1;PV1=0.38;PV2=1;PV3=0.12;PV4=1,0.38,1,0.12;QD=0.1029;SB=0.4375;VDB=0.0144;CSQ=ENSMUST00000025835:ENSMUSG00000024900:intron_variant:Allele,G:Gene,Cpt1a       GT:GQ:DP:SP:PL:FI  **1/1:99:21:0:216,0,100:1**

I apologize if I'm getting this wrong but doesn't this mean that CASTEiJ is marked to have a SNP in a deleted position wrt to the reference?

Let me know if you have some suggestions, or have some experience with this data.

vcf snp indel
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written by dfernan dfernan

Normally SNPs in the vicinity of an Indel are marked as FAIL as they can be due to mapping artifacts. I am sure they have performed the variant clean up process but I am not sure how this particular SNP survived. As they analysed the combined data of 17 strains may be they didn't flag the SNP variant as one of the strain may not have the deletion but this SNP variant. I still don't know what is going on.

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written by Ashutosh Pandey Ashutosh Pandey

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