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Basically I have an odd-looking distribution of my variant quality scores (see attached png), and was wondering how concerned should I be and how can I rectify it.
The input data from the graph is from UnifiedGenotyper vcf output file, QUAL values.
The four samples in the vcf file are one Drosophila reference line, and three more which are outcrosses of the reference line and thus are heterozygous for the reference allele.
My fastq read-mapping pipeline includes adapter and low-quality base removal, and local re-alignment. I've also attached a pdf showing read quality distribution from one of the samples which also looks a bit odd.