Detailed variantCaller plugin report

Target Regions

BED—The BED file that specifies the genomic positions of interest.

Hotspot Regions

BED—The BED file that specifies the variant alleles of interest.

Effective Regions

BED—The BED file that specifies the regions actually processed in the variantCaller run for the sample or barcode (available if read trimming is enabled).

Parameter Settings

JSON—The JSON file that contains the parameter settings used in the variantCaller run for the sample or barcode.

Mapped Reads

• BAM—The BAM file that is input to the Torrent Variant Caller Pipeline for discovering and evaluating variants. Note that realignment may be applied.

• BAI—The BAI file that contains the index information for the corresponding BAM file.

Torrent Variant Caller-Processed Reads

• BAM—The BAM file that is processed by Torrent Variant Caller. Note that read trimming and read filtering may be applied. In Tag Sequencing and Ion AmpliSeq™ HD runs, the BAM file may contain consensus reads that are obtained by compressing the reads in the mapped BAM that originate from the same DNA molecule.

• BAI—The BAI file that contains the index information for the corresponding BAM file.

Variants Calls

• VCF.GZ—The compressed VCF file that contains the variant calls.

• VCF.GZ.TBI—The index file for VCF.GZ.

• XLS—The file that contains a list of variant alleles in the tab-separated file format, which can be opened in Microsoft™ Excel™.

• COV—The file that contains coverage analysis for each variant call, which can be opened in Microsoft™ Excel™.

Variants + Non-Variant Coverage

• gVCF.GZ—The bgzip-compressed genome-VCF file that contains the variant calls.

• gVCF.GZ.TBI—The tabix index file for gVCF.GZ.

View Variant Calls in IGV

IGV—The JNLP file that can be opened using (IGV) to visualize the variant calls.