**130**wrote:

I'm confused about some numbers I get in a VCF file. This is an example:

gi|218888746|ref|NC_011770.1| 214 . G C 202 . DP=45;AF1=1;AC1=2;DP4=0,0,25,13;MQ=55;FQ=-141 GT:PL:GQ 1/1:235,114,0:99

The raw depth coverage at this positon is 53, as seen in samtools depth and confirmed in IGV, and DP=45, so I guess that 8 of the 53 reads are below the sequencing quality threshold set by samtools, which I think is q20 (Please correct me if this is wrong), My actual confusion comes when I look at the DP4 numbers which totals 38, so if DP is already quality filtered, shouldnt DP equal the sum of DP4 values? Otherwise, what is the different the "high-quality" filtering to get to the DP4 values and the filtering to get to the DP value. Thanks

**7.5k**• written 7.0 years ago by Juliofdiaz •

**130**