How Can I Make A Multi Alignment From The Vcf File Of Snp'S.

Question

[satish.nair]

Hi Everyone,

I have a VCF file of SNP,s that I called using GATK and now I need to make a multi alignment with this SNP's to do the phylogenetic analysis....

In this I can see for all samples in the Genotype section it is 1/1 or 0/1 or 0/0. I understand 0 is same as reference and 1 is the alternate.

My question is HOW can I make a multi alignment from having 2 information for a particular sample? In the sample given below the first one is chr1 824523 T C some missing reads then 1/1 0/0 . if it is 0/1 as seen in the second line of the sample I have given what will be my SNP. should I take the alternate or reference???

Thanks in advance.

This is how my VCF file looks:

chr1    824523  rs79497635      T       C       15.41   LowQual AC=4;AF=0.500;AN=8;BaseQRankSum=1.026;DB;DP=15;Dels=0.00;FS=2.632;HaplotypeScore=0.2483;MLEAC=4;MLEAF=0.500;MQ=14.52;MQ0=4;MQRankSum=0.000;QD=7.71;ReadPosRankSum=-1.026;SB=-1.728e+01  GT:AD:DP:GQ:PL  ./.     ./.     ./.     ./.     0/0:1,0:1:3:0,3,28
      ./.     1/1:0,1:1:3:28,3,0      ./.     ./.     ./.     ./.     ./.     ./.     ./.     1/1:0,1:1:3:28,3,0      ./.     ./.     ./.     ./.     ./.     ./.     ./.     0/0:1,0:1:3:0,3,34      ./.     ./.     ./.
chr1    824632  rs75185704      T       C       12.56   LowQual AC=3;AF=0.500;AN=6;BaseQRankSum=-1.231;DB;DP=12;Dels=0.00;FS=3.522;HaplotypeScore=0.0000;MLEAC=3;MLEAF=0.500;MQ=17.41;MQ0=1;MQRankSum=-1.231;QD=3.14;ReadPosRankSum=-0.358;SB=-1.975e-02        GT:AD:DP:GQ:PL  ./.     ./.     ./.     ./.     1/1:0,2:2:3:28,3,0      0/0:1,0:1:3:0,3,38      ./.     ./.     ./.     ./.     ./.     ./.     ./.     ./.     ./.     ./.     ./.     ./.     ./.     ./.     ./.     ./.     0/1:1,1:2:22:22,0,26    ./.     ./.     ./.
chr1    825069  rs4475692       G       C       20.08   LowQual AC=4;AF=1.00;AN=4;BaseQRankSum=1.026;DB;DP=18;Dels=0.00;FS=3.010;HaplotypeScore=1.3411;MLEAC=4;MLEAF=1.00;MQ=9.42;MQ0=6;MQRankSum=1.026;QD=3.35;ReadPosRankSum=0.000;SB=-1.975e-02      GT:AD:DP:GQ:PL  ./.     ./.     ./.     ./.     ./.     1/1:1,2:3:3:23,3,0      ./.     1/1:1,1:3:3:30,3,0      ./.     ./.     ./.     ./.     ./.     ./.     ./.     ./.     ./.     ./.     ./.     ./.     ./.     ./.     ./.     ./.     ./.     ./.
chr1    825207  rs61768257      T       C       48.26   LowQual AC=6;AF=1.00;AN=6;DB;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=6;MLEAF=1.00;MQ=11.27;MQ0=7;QD=9.65;SB=-1.975e-02     GT:AD:DP:GQ:PL  ./.     ./.     ./.     ./.     ./.     1/1:0,2:2:3:28,3,0      ./.     ./.     ./.     ./.     ./.     ./.     ./.     ./.     ./.     ./.     1/1:0,1:1:3:27,3,0      ./.     ./.     ./.     ./.     ./.     1/1:0,2:2:3:28,3,0      ./.     ./.     ./.

Answer 1

[Sean Davis]

You can simply load your VCF file into IGV. It "does the right thing" so you can quickly see what is going on at any given location. Alternatively, the UCSC browser supports vcf format.

http://genome.ucsc.edu/goldenPath/help/vcf.html

[satish.nair]

Hi thanks for the reply but I didnt understand fully what you meant. I actually want to make a multi alignment from the vcf file. So how can I get a value from the vcf file where we have 2 alleles for the same position. which allele should we consider and on what basis.

[Sean Davis]

I had assumed that your sample was diploid, so you do have two alleles for the same position--correct. At a given locus, a 1/1 means the sample has two alternate alleles; 0/1 means one alternate and one reference; 0/0 means both are reference. If your sample is NOT diploid, then you may want to treat 0/0 as reference and 0/1 and 1/1 as variant.

[satish.nair]

thank you. My sample is a diploid sample. So now I am confused when I have 2 alleles which one I should consider for the multi alignment at that position. If it is a 1/1 i think I can consider the alternate and 0/0 i can consider reference but if it is 0/1 then with the diploid sample how can I make the multi alignment? Sorry if I am not able to convey it as the way I wanted to.