<p>I've been working on editing some code on the server at my work, I've come into a problem where we need a snp quality to go through our filters downstream in the pipeline that we use. Does anyone know if Snp Quality exists in the VCF file? If so where? </p>

<p>SNP Quality can be represented in several places in a VCF file. </p>

<p>1) the QUAL column, which is the phred-scaled quality score for the assertion made in ALT. In other words, it's: 10log_10 prob(call in ALT is wrong). </p>

<p>2) GQ, encoded in the FORMAT column is genotype quality, encoded as a phred score: -10log_10p(genotype call is wrong). </p>

<p>3) Especially if you're looking at tumor/normal pairs, you may see that it's represented as VAQ (variant quality).</p>

<p>The header of the VCF should give a description of exactly which fields are present in your files and help you determine which ones contain the quality scores that you're looking for.</p>

<p>For more info, check out the <a href='http://www.1000genomes.org/node/101'>VCF format description</a></p>
