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Torrent Browser Analysis Report Guide

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Analysis Report Guide TOC

The Command-Line Torrent Variant Caller

This version of the Torrent Variant Caller (TVC) is run on the Linux command-line and does not have a UI interface.

The command-line TVC is supported only on Torrent Server (release 4.2 or higher) and requires an input BAM file of Ion Torrent data.

Example command

The following is an example TVC command. The options are described in the table after the example. 

             ### Put your own values in these variables
BEDS=/results/uploads/BED/22/hg19
DIR=your_directory
INPUT=$DIR/yourBAM.bam
PARAMFILE=somatic_lowstringency_pgm_parameters.json
###


TVCDIR=/results/plugins/variantCaller
OUT=$DIR/out
BAM=`echo $(basename $INPUT)  | sed -e 's/.bam$//'`
echo $BAM

$TVCDIR/variant_caller_pipeline.py  \
   --input-bam $BAM \
   --reference-fasta /results/referenceLibrary/tmap-f3/hg19/hg19.fasta \
   --output-dir $OUT/$BAM \
   --parameters-file $TVCDIR/pluginMedia/parameter_sets/$PARAMFILE \
   --input-bam $BAM \
   --postprocessed-bam $OUT/$BAM/PTRIM.bam \
   --primer-trim-bed $BEDS/unmerged/detail/designed.bed \
   --bin-dir /results/plugins/variantCaller \
   --hotspot-vcf $DIR/hotspots.vcf.gz \
   --region-bed  $BEDS/merged/plain/designed.bed  > $OUT/$BAM/log.txt 2>&1

Supported options

Many options have two equivalent versions. Choose the version that you prefer but use only one of the versions. Example:

  • -b BEDFILE
  • --region-bed=BEDFILE

Option Description

-h

--help

Show options in a help message and exit

-b BEDFILE

--region-bed=BEDFILE

Limit variant calling to regions in this BED file. Optional.

-s HOTSPOT_VCF

--hotspot-vcf=HOTSPOT_VCF

VCF.gz (+.tbi) file specifying exact hotspot positions . Optional.

-i BAMFILE

--input-bam=BAMFILE

BAM file containing aligned reads

-r REFERENCE

--reference-fasta=REFERENCE

FASTA file containing reference genome

-o OUTDIR

--output-dir=OUTDIR

Output directory. Optional. Uses the current directory if this option is missing.

-p PARAMFILE

--parameters-file=PARAMFILE

JSON file containing variant calling parameters. Optional but recommended.

-B RUNDIR

--bin-dir=RUNDIR

Directory path to location of variant caller programs. Optional. Uses the directory where the variant_caller_pipeline.py script is located, if this option is missing.

-n NUMTHREADS

--num-threads=NUMTHREADS

Sets the number of threads used by the TVC process. Optional. D efaults to 12, if this option is missing.
--postprocessed-bam=PTRIM_BAM

Perform primer trimming, storing the results in provided BAM file name. Optional.

Requires the --primer-trim-bed option.

--primer-trim-bed=PTRIM_BED BED file used for primer trimming. Required if --primer-trim-bam is used.

About target regions BED files

When a target regions BED file is uploaded to torrent servers, it is converted into 4 different versions: merged and unmerged, plain and detailed.

The merged plain version has the duplicate regions merged or removed. Use the merged plain BED file with the TVC --region-bed option to avoid redundant variant calls being made.

Use the unmerged detail version of the BED file with the TVC --primer-trim-bed option.

You can find the converted bed files under /results/uploads/BED/ . The directory structure is shown in this example: 

             ./22/hg19/merged/plain/ColonLung.20131001.designed.bed
./22/hg19/merged/detail/ColonLung.20131001.designed.bed
./22/hg19/unmerged/plain/ColonLung.20131001.designed.bed
./22/hg19/unmerged/detail/ColonLung.20131001.designed.bed

Contents

Torrent Browser Analysis Report Guide

Run Report Metrics

Run Metrics Overview

Run Report Metrics Before Alignment

Run Report Metrics on Aligned Reads

Compare Multiple Run Reports

Barcode Reports

Test Fragment Report

Report Information

Output Files

Plugin Summary

Run the Installed Plugins

Assembler SPAdes Plugin

Coverage Analysis Plugin

ERCC Analysis Plugin

FileExporter Plugin

FilterDuplicates Plugin

IonReporterUploader Plugin

See The Ion Reporter™ Software Integration Guide

Run RecognitION Plugin

SampleID Plugin

TorrentSuiteCloud Plugin

Torrent Variant Caller Plugin

Torrent Variant Caller Parameters

  Example Torrent Variant Caller Parameter File

Torrent Variant Caller Output

The Command-Line Torrent Variant Caller

  Ion Reporter™ Software Features Related to Variant Calling

Integration with TaqMan® and PCR

Classic Run Reports