Setting | Description |
|---|---|
Consensus | Selected by default. Do local indel realignment based on the consensus sequence. After variant calls are made based on the initial alignment, any reads that overlap indels but do not contain the indels are adjusted to include the indels if the new alignment is at least as good as the initial alignment. |
Remove PCR Duplicates | Reads are identified as PCR duplicates based on their start positions. If you are using paired-end data, then each pair of reads is considered together. If you leave the option unselected, then the PCR duplicates are not removed; otherwise, select the option to remove PCR duplicates. Note: If you are using targeted sequencing, then you typically do not select this value. If you are using whole genome sequencing, then you typically do select this value. |
Keep Only Proper Pairs | Ignore any reads that were not marked as being part of a proper pair, where a proper pair is defined as the following: • Both reads from the pair must be aligned and the alignment must be on opposite strands. • The 5’ end of the reverse read must be to the right of the 5’ end of the forward read. |
Merge Pairs | Applicable only for mtDNA data that does not use a panel. If the reads are expected to fully overlap, then Merge Pairs is appropriate for mtDNA data. If you select Merge Pairs, then the overlapped portion of pairs is combined, which reduces coverage; however, because double counting is prevented, accuracy might be improved. If you select Merge Pairs, then the following options are enabled, and you can select one: • Pre-alignment merging: Selected by default. Results in slower data analysis and is more prone to error, especially in repetitive regions, but for certain situations such as those that involve high quality data and/or sequences that are not highly repetitive, then selecting this option can improve alignment. • Post-alignment merging: Because the reads might already be correctly overlapped after alignment, selecting this option results in faster data analysis. Tip: If you are not sure as to which option to select, analyze the data using both options, compare the results, and then make your selection. |
Motifs | Selected by default. The alignments of reads that cross motif regions with expected sequences are adjusted to match the list of variants. See Overview of using a motif. Note: This is a default setting for all the Sequencer options (Ion Torrent, Illumina, and Other). If you do not want to use motifs, then you must manually clear this option. |