GATK HaplotypeCaller

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Quick Start

To use GATK HaplotypeCaller, import your preprocessed alignment output data in BAM format and reference genome in fasta format.
*Resources: https://www.broadinstitute.org/gatk/guide/tooldocs/org_broadinstitute_gatk_tools_walkers_haplotypecaller_HaplotypeCaller.php

Test Data

Test data for this app appears directly in the Discovery Environment in the Data window under Shared With Me” -> luj -> variant_calling.

Input File(s)

Use directory picard_preprocess_output from the directory above as input directory of preprocessed bam files.
Use ricen_Chr12.fa as reference genome fasta file.
Use ricen_Chr12_target.intervals as samtools-style intervals of targets

Parameters Used in App

When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.

Default parameters only, no further configuration needed.

Advanced Use

The preprocessed bam file should be bam file that has been sorted, deduped, and read group info added.
You could limit the analysis to target regions in a samtools-style intervals file
You could provide known variants, such as dbsnp, in a vcf file
You could set following parameters of analysis
- The minimum phred-scaled confidence threshold at which variants should be called (-stand_call_conf)
- The minimum phred-scaled confidence threshold at which variants should be emitted (-stand_emit_conf)

Output File(s)

Expect a directory named gatk_haplotypecaller_output as output directory containing the vcf output files.

Tool Source for App

https://www.broadinstitute.org/gatk/guide/tooldocs/org_broadinstitute_gatk_tools_walkers_haplotypecaller_HaplotypeCaller.php

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