This rounding may lead to different duplicate marks from those chosen by Picard, but because the reads were very close in quality this has negligible impact on variant calling results. This score is stored as a one-byte number, with values rounded down to the nearest one-quarter. Simply click a column header to sort by that column click again to reverse the sort order. Note that 'unknown' will still be presented if the security. As with all File Reports, the Duplicate Files report can be sorted by any column in either ascending or descending order. Feature: When Duplicate File Detective encounters a file system security identifier that is not mapped to an account name, it will now convert the SID to a string (e.g. QUAL is its array of Phred quality scoresĭedup-min-qual is a DRAGEN configuration option with default value of 15.įor a pair, the score is the sum of the scores for the two ends. Once the Duplicate Files report has been generated, duplicate files are displayed in groups. Pictured: former Louisville Metro Police Detective Mark Handy in court for sentencing on May 11, 2021. These commands produce qualitatively different data. Use the following commands to flag duplicates for 6747snippet.bam. The score for an unpaired read R is the average Phred quality score per base, calculated as follows: Again, the duplicate scoring methods differ for each tool. If there are multiple pairs that also tie on this attribute, then DRAGEN chooses a pairarbitrarily. If two reads (or pairs) have exactly matching quality scores, DRAGEN breaks the tie by choosing the pair with the higher alignment score. Dead on time book by meghnad desai, 6 1/2 pitch roof, Mark 42 diecast hot. The score is intended to preserve the reads with the highest-quality base calls. Pairs receive the sum of the scores of both ends, while unpaired reads get the score of the one mapped end. For this comparison, duplicates are scored based on the average sequence Phred quality. When DRAGEN identifies a group of duplicates, it picks one as the best of the group, and marks the others with the BAM PCR or optical duplicate flag (0x400, or decimal 1024). Unmapped or read pairs are never marked as duplicates. In addition, an unpaired read may be marked as a duplicate if it has identical coordinate and orientation with either end of any other read, whether paired or not. Identical orientations (direction of the two ends, with the left-most coordinate being first). Identical alignment coordinates (position adjusted for soft- or hard-clips from the CIGAR) at both ends. Dana Smark's Phone Number and Email Last Update. All the aligned reads are grouped into subsets in which all the members of each subset are potential duplicates.įor two pairs to be duplicates, they must have the following: Dana Smark is a Detective at Montgomery County Texas based in Montgomery, Texas. The DRAGEN duplicate-marking algorithm is modeled on the Picard toolkit MarkDuplicates feature.
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