Sentence examples for minimum mapping quality from inspiring English sources

A set of custom scripts and samtools (v 0.1.18) were used to filter reads to obtain reads that mapped uniquely, allowing up to three mismatches, minimum mapping quality of 10, minimum and maximum insert size of 150 and 1 000 000, respectively.

SNPs were filtered using vcfutils.pl varFilter with minimum mapping quality (-Q) of 20 and minimum and maximum read coverage of 20 and 100 respectively.

All reads with a minimum mapping quality of at least 20 were used as single read data and converted into a fastq file.

Overall 96% of inserts with a minimum mapping quality of 10 were mapped on either the pig genome sequence (Build 8) or the PRV genome, and 88.9% of the reads could be aligned with a mapping quality of 40 or higher.

Read alignments were filtered for a minimum mapping quality (MAPQ) of 20 before further analysis.

Variants and genotypes were called using the HaplotypeCaller tool from the GATK (v2.7-2) (McKetnalet al. 2010) with a minimum mapping quality threshold of 25.

For in-house genomes, SNP calls were then made by using SolSNP version 1.1 with the following alignment limits: minimum coverage of 20, minimum mapping qualities of 20, and a filter call of 0.95.

Only a few thresholds were incorporated within the commands for the initial calling of the variants, viz., minimum base quality of 20, minimum map quality of 20 and InDel alleles supported by at least two reads.

Default maq parameters were used for SNP calling and for filtering as described in the maq paper, (maq.pl SNPfilter -f cns.indelse -F cns.indelpe -d 3 -q 40 -Q 60 -w 5 -N 2), with a subsequent minimum map quality filter of 30 applied after the indel proximity filters.

Single-base substitutions were called using SAMtools and filtered by coverage (minimum 10, maximum 150), read quality (minimum quality, 30), mapping quality (minimum quality, 30), base quality (minimum quality, 30), and end of contig (minimum distance to end of contig, 500 bp).

First, raw SNP calls from the pipeline were filtered with the maq.pl SNP filter script using a minimum depth of 20 reads, a maximum depth of 225, a minimum consensus score of 30, a minimum adjacent consensus score of 20, and a required maximum mapping quality of 60.