Sentence examples for minimal mapping quality from inspiring English sources

SNPs were called only for positions with a minimal mapping quality (-Q) of 20, and maximum read depth (-D) was set at 200.

To minimize possible sources of false positive in variant calling, we only kept ~23 million aligned reads (12.4%) in total with a minimal mapping quality score of 30.

For each strain, we calculated a per-locus depth-of-coverage using GATK (McKenna et al., 2010), with a minimal mapping quality of 10.

The SAMtools pileup command was used for variant detection in BWA pipeline with default parameters but for filtering, a minimal mapping quality of 20 was used.

The SAMtools pileup command was used for variant detection in SMALT pipelines with default parameters but for filtering a minimal mapping quality of 20 was used.

The minimal mapping quality of the reads that Pindel uses as anchor was set to 20 (parameter "A") and the maximum size of SV to be detected was set to 32,628 bp (parameter "x").

Specifically, MAQ's minimal map quality for the read, minimal consensus quality and minimal map quality of the best mapping read for each predicted SNP position were used as criteria to select reliable SNPs by setting the thresholds for all three parameters at 10 (SNPs with any values<10 were discarded).

Further criteria used to exclude less reliable SNPs from the dataset included a minimal map quality for the read of 10, minimal consensus quality of 10 and a minimal map quality of the best mapping read of 10 for each predicted SNP position.

We filtered the MAQ [ 30] SNP output according to several rules: minimal map quality per read: 10; minimal map quality of the best mapping read on a SNP position: 10; maximum read depth at the SNP position: four times the actual coverage after quality filtering; minimum consensus quality: 10 [ 22].

SA006 and SA035 do display an increased duplicate rate (54%, 78% respectively), but SA008 also displays high duplicate rate with minimal effect on mapping quality.

Reads with mapping quality zero were discarded.