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I got VCF file for a sample (Bam file-RNAseq) using HaplotypeCaller. After extract known SNPs (with rs ID) I have the frequency of each genotype as follows:
0/0 = 6036
0/1 = 421480
1/1 = 777386
0/2 = 501
1/2 = 1571
2/2 = 113
./. = 369
Total: 1,207,456 SNPs
The questions are :
1) Why the frequency of reference homozygous (0/0) is so low (0.5%) and for the Alternative is very high (64%)?
2) I checked and compared some "Ref" and "ALT" alleles in VCF with NCBI website. They are exactly the opposite reported. Why?
3)The highest rate of callvariants achieved when DP=2. why? The range of DP in my VCF file is 1-to-446.