Showing docs for version 3.7-0

AnalyzeCovariates

Create plots to visualize base recalibration results

Category Diagnostics and Quality Control Tools

Traversal LocusWalker

PartitionBy LOCUS

Overview

This tool generates plots for visualizing the quality of a recalibration run (effected by BaseRecalibrator).

Input

The tool can take up to three different sets of recalibration tables. The resulting plots will be overlaid on top of each other to make comparisons easy.

Set	Argument	Label	Color	Description
Original	-before	BEFORE	Pink	First pass recalibration tables obtained from applying BaseRecalibration on the original alignment.
Recalibrated	-after	AFTER	Blue	Second pass recalibration tables results from the application of BaseRecalibration on the alignment recalibrated using the first pass tables
Input	-BQSR	BQSR	Black	Any recalibration table without a specific role

You need to specify at least one set. Multiple sets need to have the same values for the following parameters:

covariate (order is not important), no_standard_covs, run_without_dbsnp, solid_recal_mode, solid_nocall_strategy, mismatches_context_size, mismatches_default_quality, deletions_default_quality, insertions_default_quality, maximum_cycle_value, low_quality_tail, default_platform, force_platform, quantizing_levels and binary_tag_name

Output

A pdf document with plots that show the quality of the recalibration, and an optional csv file that contains a table with all the data required to generate those plots.

Usage examples

Plot a single recalibration table

 java -jar GenomeAnalysisTK.jar \
      -T AnalyzeCovariates \
      -R myrefernce.fasta \
      -BQSR myrecal.table \
      -plots BQSR.pdf

Plot before (first pass) and after (second pass) recalibration tables to compare them

 java -jar GenomeAnalysisTK.jar \
      -T AnalyzeCovariates \
      -R myrefernce.fasta \
      -before recal2.table \
      -after recal3.table \
      -plots recalQC.pdf

Plot up to three recalibration tables for comparison


 # You can ignore the before/after semantics completely if you like (if you do, add -ignoreLMT
 # to avoid a possible warning), but all tables must have been generated using the same parameters.

 java -jar GenomeAnalysisTK.jar \
      -T AnalyzeCovariates \
      -R myrefernce.fasta \
      -ignoreLMT \
      -BQSR recal1.table \   # you can discard any two
      -before recal2.table \
      -after recal3.table \
      -plots myrecals.pdf

Full BQSR quality assessment pipeline

 # Generate the first pass recalibration table file
 java -jar GenomeAnalysisTK.jar \
      -T BaseRecalibrator \
      -R reference.fasta \
      -I myinput.bam \
      -knownSites bundle/my-trusted-snps.vcf \ # optional but recommended
      -knownSites bundle/my-trusted-indels.vcf \ # optional but recommended
      -o firstpass.table

 # Generate the second pass recalibration table file
 java -jar GenomeAnalysisTK.jar \
      -T BaseRecalibrator \
      -R reference.fasta \
      -I myinput.bam \
      -knownSites bundle/my-trusted-snps.vcf \
      -knownSites bundle/my-trusted-indels.vcf \
      -BQSR firstpass.table \
      -o secondpass.table

 # Finally generate the plots and also keep a copy of the csv (optional)
 java -jar GenomeAnalysisTK.jar \
      -T AnalyzeCovariates \
      -R reference.fasta \
      -before firstpass.table \
      -after secondpass.table \
      -csv BQSR.csv \ # optional
      -plots BQSR.pdf

Additional Information

Read filters

These Read Filters are automatically applied to the data by the Engine before processing by AnalyzeCovariates.

Command-line Arguments

Engine arguments

All tools inherit arguments from the GATK Engine' "CommandLineGATK" argument collection, which can be used to modify various aspects of the tool's function. For example, the -L argument directs the GATK engine to restrict processing to specific genomic intervals; or the -rf argument allows you to apply certain read filters to exclude some of the data from the analysis.

CommandLineGATK

AnalyzeCovariates specific arguments

This table summarizes the command-line arguments that are specific to this tool. For more details on each argument, see the list further down below the table or click on an argument name to jump directly to that entry in the list.

Argument name(s)	Default value	Summary
Optional Inputs
--afterReportFile -after	NA	file containing the BQSR second-pass report file
--beforeReportFile -before	NA	file containing the BQSR first-pass report file
Optional Outputs
--intermediateCsvFile -csv	NA	location of the csv intermediate file
--plotsReportFile -plots	NA	location of the output report
Optional Flags
--ignoreLastModificationTimes -ignoreLMT	false	do not emit warning messages related to suspicious last modification time order of inputs

Argument details

Arguments in this list are specific to this tool. Keep in mind that other arguments are available that are shared with other tools (e.g. command-line GATK arguments); see Inherited arguments above.

--afterReportFile / -after

file containing the BQSR second-pass report file
File containing the recalibration tables from the second pass.

File NA

--beforeReportFile / -before

file containing the BQSR first-pass report file
File containing the recalibration tables from the first pass.

File NA

--ignoreLastModificationTimes / -ignoreLMT

do not emit warning messages related to suspicious last modification time order of inputs
If true, it won't show a warning if the last-modification time of the before and after input files suggest that they have been reversed.

boolean false

--intermediateCsvFile / -csv

location of the csv intermediate file
Output csv file name.

File NA

--plotsReportFile / -plots

location of the output report
Output report file name.

File NA