Hi,
I used samtools pileup (0.1.7) and mpileup/bcftool (0.1.14) to call SNPs for my datasets. And we also perform taqman assay of one SNP for the same 28 samples. (One SNP is a small sample, however I still compare the results between samtools and taqman assay.)
We found that results of old version with pileup can match 27/28 samples from Taqman; results of new version with mpileup can only match 7/28 samples from taqman. So old version seems to be better for my dataset. Did anybody do the similar validation before? What is your conclusion?
Thanks!
I used samtools pileup (0.1.7) and mpileup/bcftool (0.1.14) to call SNPs for my datasets. And we also perform taqman assay of one SNP for the same 28 samples. (One SNP is a small sample, however I still compare the results between samtools and taqman assay.)
We found that results of old version with pileup can match 27/28 samples from Taqman; results of new version with mpileup can only match 7/28 samples from taqman. So old version seems to be better for my dataset. Did anybody do the similar validation before? What is your conclusion?
Thanks!
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