LightSpeed Fastq to Somatic Variants Tumor Normal

The LightSpeed Fastq to Somatic Variants Tumor Normal tool is designed to provide somatic variant calls from a tumor and a normal sample within a very short timeframe.

The tool can perform read trimming, mapping, deduplication, local realignment and variant calling. For a description of each step, see LightSpeed Methods.

LightSpeed Fastq to Somatic Variants Tumor Normal can only analyze one sample per analysis start (see Batching).

To run the tumor normal LightSpeed tool go to:

        Tools | LightSpeed (Image lightspeed_folder_open_16_n_p) | LightSpeed Fastq to Somatic Variants Tumor Normal (Image var_ls_16_n_p)

If you are connected to a CLC Server via your Workbench, you will be asked where you would like to run the analysis. We recommend that you run the analysis on a CLC Server when possible.

In the first wizard step, specify tumor and normal fastq files and a reference sequence (figure 3.12):

Image lis_tumor_normal_step1
Figure 3.12: Input fastq files and references, and, optionally, a track for reference masking.

Next, options are available for trimming (figure 3.13):

Image lis_tumor_normal_step2
Figure 3.13: Options for trimming.

Next, options are available for UMI and duplicate reads (figure 3.14):

If UMIs are defined on both read 1 and read 2, the data is considered duplex. Consequently, simplex UMI reads sharing a UMI and mapping position that originate from different strands will be collapsed to a duplex UMI read.

Image lis_tumor_normal_step3
Figure 3.14: Options for UMI and duplicate reads.

Next, options are available for primer trimming (figure 3.15):

Image lis_tumor_normal_step4
Figure 3.15: Options for primer trimming.

A number of options are available for variant detection in the next two wizard steps (figure 3.16 and figure 3.17).

Image lis_tumor_normal_step5
Figure 3.16: The first wizard step containing options for variant detection.

For the options under Variant detection general filters and Variant detection noise filters

Image lis_tumor_normal_step6
Figure 3.17: The second wizard step containing options for variant detection.

In the following wizard step, specify the maximum variant count, frequency and significance in the normal read mapping (figure 3.18).

Image lis_tumor_normal_step7
Figure 3.18: The first wizard step containing options for variant detection.

In the final wizard step, choose which outputs should be generated and whether results should be saved or opened. If a reads track is selected as output, runtime will increase.



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