Setting | Description |
|---|---|
Match Proportion | Include the read if the proportion of the read that is aligned and not soft-clipped is greater than or equal to the indicated value, where the default value is Percent >=90. Note: Soft-clipping can be carried out only if the proportion of the read that is aligned and not soft-clipped is greater than or equal to the indicated value. Tip: You should set this value to < 90% if you have a larger number of variants in the middle for the reads and you need more reads to align. Conversely, if your reads are of higher quality, particularly for the ends, then less reads need to align and you can set this to value to >90%. |
Identity | Reads that are less similar to the reference than indicated value are not aligned. Select the way to identify the number of reads: • Percent >=: Selected by default. Default value is 90. If the percentage of reads for a sample that do not match the reference are greater than or equal to the indicated value, then reads are not aligned. • Number <=: Default value is 0. If the total number of reads for a sample that align to reference are less than or equal to the indicated value, then the reads are not aligned. |
Soft Clipping at 3’ Q < | When the base call quality is less than or equal to the indicated quality score, then the 3’ ends of reads are trimmed accordingly. See Soft clipping based on quality scores. |
Note: GeneMarkerHTS automatically adjusts the default values for both Identity and Soft Clipping based on the selected sequencer. The default settings are based on using an Illumina or Ion Torrent sequencer. If you change the value for either one or both of the settings, then GeneMarkerHTS automatically selects “Other” for Sequencer. | |
Clip mismatched ends | Selected by default. If mismatched bases are found near the end of the alignment, then soft clipping is also carried out on the 3’ ends of reads. Tip: When carrying out panel analysis for mtDNA amplicons, you can clear this option to improve trimming if variants are at a boundary. |