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GATK different from Sanger results
Below are two SNPs I obtained for two samples from Exom DNAseq and Sanger.
From Sanger's results, it seems both SNPs are heterozygous, while GATK(v3.2) call one sample as homozygous.
Both SNP's VQSLOD > 6, does this mean we still need to do filtering based on sequencing depth, which is hard filtering, then why do we need the machine learning-based soft filtering?
If we need to do filtering based on sequencing depth, what threshold would you recommend?
Sample1:GATK Sample2:GATK Sanger for both samples Sample1:IGV Sample2:IGV
CT T C,T C:9,T:2 T:9
T GT G,T T:7 G:7,T:8