SNP and allele concept

[bio_jit]

I did exom sequencing and annotate the VCF

now I have somthing like this

chr Ref Alt condition
chr1 A G Het

Chr = chromosome
Ref = reference allele
Alt = alternate allele observed in my sample
Condition = hetero means what? few samples have G and few have something else in same position? how do i explain?

If I want to code this is like AA GG form how do i code hetero?

please answer

[hkeward]

Heterozygotes in your example will have 1 ref and 1 alt allele. They would be coded AG or GA.
If you restricted your vcf to biallelelic results all heterozygotes will take that form. If there are some sites where more than one alt allele exists, there are a number of combinations of ref/alt1/alt2..altn that could exist. The best place to look to understand what's going on is the genotype (GT) field.

[bio_jit]

thanks for your reply. I have another query related to VCF annotation

I used GATK pipeline with haplotypecaller for somatic mutation, I annotate control and treated sample separately and annotating each vcf separately with wAnnovar. am I doing wrong?

If I merged the VCF files (control and treated) and then doing annotation I am not getting any information about which SNP in which sample. But, merged vcf file have sample information.

please help