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GATK 3.3 UG question regarding DP in info and sample field.
We are trying to determine positions with low coverage using GATK 3.3 UnifiedGenotyper. Although there are walkers for this that may be more appropriate, the way the pipeline was originally set up in 2011 was to use the allbase vcf file and to pull DP. We have many clinically important genes with high homology and thus poor mapping quality reads. I was under the assumption that the DP in the FORMAT fields was filtered and thus would remove low MQ reads. However, this appears not to be the case and it looks like there is adequate good quality coverage at these positions (see below). Can you help clarify this?
14 23859426 . G . 241.23 . AN=2;DP=978;MQ=10.50;MQ0=904 GT:DP 0/0:978
14 23859427 . C . 241.23 . AN=2;DP=976;MQ=10.51;MQ0=902 GT:DP 0/0:976
14 23859428 . A . 238.23 . AN=2;DP=978;MQ=10.65;MQ0=902 GT:DP 0/0:978
14 23859429 . G . 241.23 . AN=2;DP=970;MQ=10.54;MQ0=896 GT:DP 0/0:970