Interpretting QUAL/DP4 in VCF files
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]
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
understanding pysam.AlignmentFile output
written by bitpir
-
Interpreting bbduk histogram headers and contents
written by gnmcsbnfrmtcsclb •
-
working with Sanger fasta + qual + clip files
written by sullis02 •
-
MGRA returns error
written by little_more •
-
Algorithm for Getting per position nucleobases in python from bam file
written by ammarsabir15
-
QUAL value from .vcf file is the phred score
written by cmatho •
-
Pysam (python) problem parsing BAM reference id
written by liorglic
-
(samtools) Filtering and interpreting >100 QUAL scores
written by umn_bist •
-
Need help understanding read depth for somaticsniper vcf's
written by Jordan
-
How to trim ngs sequences according to the phred score using python/biopython
written by linlinli99013 •
