You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
I used GATK4 detection to obtain a large number of SNPs, but I found many wrong SNPs when I randomly selected some SNPs to verify the accuracy of the detection. For example, I got a site (Chr01_202655, alleles: C/T) in sample 1 which is C. But when I check it in the sorted bam file using the "samtools tview", I find that it is a heterozygote site (alleles: Y). And these wrong SNPs found are often concentrated in some areas. I don't know why this is happening?
reacted with thumbs up emoji reacted with thumbs down emoji reacted with laugh emoji reacted with hooray emoji reacted with confused emoji reacted with heart emoji reacted with rocket emoji reacted with eyes emoji
-
I used GATK4 detection to obtain a large number of SNPs, but I found many wrong SNPs when I randomly selected some SNPs to verify the accuracy of the detection. For example, I got a site (Chr01_202655, alleles: C/T) in sample 1 which is C. But when I check it in the sorted bam file using the "samtools tview", I find that it is a heterozygote site (alleles: Y). And these wrong SNPs found are often concentrated in some areas. I don't know why this is happening?
Beta Was this translation helpful? Give feedback.
All reactions