Variant Effect Predictor For Two Individuals Output

Question

[Houkto]

Hi, am using Ensembl Virtual Machine 71 Variant Effect Predictor (VEP) to annotate NGS whole genome sequence variants from two individuals. The input VCF file has both unqiue and common SNPs between the two samples and I am more interested in what is unique between the two only when compared to reference genome.

VCFv4.1 sample

#CHROM    POS    ID    REF    ALT    QUAL    FILTER    INFO    FORMAT    IND1    IND2
1    615519    .    C    T    721.4    PASS    AC=2;AF=0.500;AN=4;BaseQRankSum=-0.462;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=3;MLEAF=0.750;MQ=58.11;MQ0=0;MQRankSum=1.271;QD=24.88;ReadPosRankSum=1.040    GT:AD:DP:GQ:PL    1/1:0,29:29:69:782,69,0    0/0:1,0:1:3:0,3,32
1    87593200    rs197529280    C    A,T    1288    PASS    AC=2,2;AF=0.500,0.500;AN=4;DB;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2,2;MLEAF=0.500,0.500;MQ=59.63;MQ0=0;QD=25.25    GT:AD:DP:GQ:PL    1/1:0,34,0:34:78:936,78,0,936,78,936    2/2:0,0,17:17:51:548,548,548,51,51,0
1    2863220    .    A    C,G    1791.73    PASS    AC=3,1;AF=0.750,0.250;AN=4;DP=94;Dels=0.00;FS=0.000;HaplotypeScore=0.4470;MLEAC=3,1;MLEAF=0.750,0.250;MQ=59.01;MQ0=0;QD=19.06    GT:AD:DP:GQ:PL    1/1:0,43,5:46:18:1058,93,0,983,18,974    1/2:0,35,11:44:99:1115,244,151,871,0,844
1    282540299    .    A    T    288.2    PASS    AC=3;AF=0.750;AN=4;BaseQRankSum=1.004;DP=14;Dels=0.00;FS=3.256;HaplotypeScore=0.0000;MLEAC=3;MLEAF=0.750;MQ=59.44;MQ0=0;MQRankSum=-0.091;QD=20.59;ReadPosRankSum=1.917    GT:AD:DP:GQ:PL    1/1:2,4:6:47:95,0,47    1/1:0,8:8:24:253,24,0

Problem: The output of VEP for the two sample using the flag --individual all will contain common SNPs with the same genotype (see line 5) or different genotype (see line 3,4) from two samples and will annotate it in two different lines; one for each individual.

Question: Can I filter what the common SNP with same genotype from the two individuals in the VCF (a command line) or VEP using an addtional flag or plugin? while the output of common SNP with different genotype (or all the SNPs) from the two samples be in one line:

SNP Variant    Chr    FromPostion    End    Reference-allele     Alternate-Allele    IND1    IND2
1_9612728_G/A    1    9612727    9612728    G    A    2    1

in which 2 mean homozygous for alternate allele, 1 heterozygous for alternate allele and 0 is the same as reference allele.

Thanks.

Answer 1

[vlad1]

You can try to use GEMINI to search VEP output with various disease association models (recessive,dominant, compound etc.).