g**********y
发帖数: 423 | 1 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.
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
C,T T C,T C:9,T:2 T:9
T G,T G,T T:7 G:7,T:8 | l********e
发帖数: 415 | 2 NGS has a much higher error rate. This is just a sequencing error, I think.
Trust the sanger result. | s******r
发帖数: 1245 | 3 看一下vcf里每个位点的depth和quality score多少，可能太低默认扔掉了
sanger是怎么做的？光看peak overlap不能知道percentage，要准的话得做subcloning
然后测几十个克隆
2)
soft
【在 g**********y 的大作中提到】
: 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.
: 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
: C,T T C,T C:9,T:2 T:9
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