Entering edit mode
7.9 years ago
dchen71
•
0
I need some help in interpreting what the QUAL and DP4 in VCF files mean. So from what I understand, QUAL is the phred score of how likely a variant is a variant wheras DP4 shows the number of reads that have the reference or alternative allele.
What I am confused by is, should the two columns be related?
For example, shouldn't the quality of these be similar?
QUAL: 228 DP4: [0, 0, 28, 36]
QUAL: 33.9413 DP4:[0, 0, 25, 35]
Another example, why is this score so high when variant alleles are skewed towards the forward?
QUAL: 228 DP4:[0, 0, 41, 4]
