AnalyzeCovariates

Evaluate and compare base quality score recalibration (BQSR) tables

Category Diagnostics and Quality Control

Overview

Evaluate and compare base quality score recalibration tables

This tool generates plots to assess the quality of a recalibration run as part of the Base Quality Score Recalibration (BQSR) procedure.

Summary of the BQSR procedure

The goal of this procedure is to correct for systematic bias that affects the assignment of base quality scores by the sequencer. The first pass consists of calculating error empirically and finding patterns in how error varies with basecall features over all bases. The relevant observations are written to a recalibration table. The second pass consists of applying numerical corrections to each individual basecall based on the patterns identified in the first step (recorded in the recalibration table) and writing out the recalibrated data to a new BAM or CRAM file.

Inputs

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	Maroon1	First pass recalibration tables obtained from applying {@link org.broadinstitute.hellbender.transformers.BQSRReadTransformer} on the original alignment.
Recalibrated	-after	AFTER	Blue	Second pass recalibration tables results from the application of {@link org.broadinstitute.hellbender.transformers.BQSRReadTransformer} 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

Outputs

Currently this tool generates two outputs:

-plots my-report.pdf: A pdf document that encloses plots to assess the quality of the recalibration
-csv my-report.csv: A csv file that contains a table with all the data required to generate those plots

You need to specify at least one of them.

Usage examples

Plot a single recalibration table

   gatk AnalyzeCovariates \
     -bqsr recal1.table \
     -plots AnalyzeCovariates.pdf

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

   gatk AnalyzeCovariates \
     -before recal1.table \
     -after recal2.table \
     -plots AnalyzeCovariates.pdf

Plot up to three recalibration tables for comparison

   gatk AnalyzeCovariates \
     -bqsr recal1.table \
     -before recal2.table \
     -after recal3.table \
     -plots AnalyzeCovariates.pdf

Notes

Sometimes you may want to compare recalibration tables where the "after" table was actually generated first. To suppress warnings about the dates of creation of the files, use the `--ignore-last-modification-times` argument.
You can ignore the before/after semantics completely if you like, but all tables must have been generated using the same parameters.

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 Tool Arguments
--after-report-file -after		file containing the BQSR second-pass report file
--arguments_file		read one or more arguments files and add them to the command line
--before-report-file -before		file containing the BQSR first-pass report file
--bqsr-recal-file -bqsr		Input covariates table file for on-the-fly base quality score recalibration
--gcs-max-retries -gcs-retries	20	If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection
--gcs-project-for-requester-pays		Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be accessed. User must have storage.buckets.get permission on the bucket being accessed.
--help -h	false	display the help message
--ignore-last-modification-times	false	do not emit warning messages related to suspicious last modification time order of inputs
--intermediate-csv-file -csv		location of the csv intermediate file
--plots-report-file -plots		location of the output report
--version	false	display the version number for this tool
Optional Common Arguments
--gatk-config-file		A configuration file to use with the GATK.
--QUIET	false	Whether to suppress job-summary info on System.err.
--tmp-dir		Temp directory to use.
--use-jdk-deflater -jdk-deflater	false	Whether to use the JdkDeflater (as opposed to IntelDeflater)
--use-jdk-inflater -jdk-inflater	false	Whether to use the JdkInflater (as opposed to IntelInflater)
--verbosity	INFO	Control verbosity of logging.
Advanced Arguments
--showHidden	false	display hidden arguments

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.

--after-report-file / -after

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

File null

--arguments_file

read one or more arguments files and add them to the command line

List[File] []

--before-report-file / -before

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

File null

--bqsr-recal-file / -bqsr

Input covariates table file for on-the-fly base quality score recalibration
Enables recalibration of base qualities, intended primarily for use with BaseRecalibrator and ApplyBQSR (see Best Practices workflow documentation). The covariates tables are produced by the BaseRecalibrator tool. Please be aware that you should only run recalibration with the covariates file created on the same input bam(s).

File null

--gatk-config-file

A configuration file to use with the GATK.

String null

--gcs-max-retries / -gcs-retries

If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection

int 20 [ [ -∞ ∞ ] ]

--gcs-project-for-requester-pays

Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be accessed. User must have storage.buckets.get permission on the bucket being accessed.

String ""

--help / -h

display the help message

boolean false

--ignore-last-modification-times

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