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Test data for this app appears directly in the Discovery Environment in the Data window under Shared With Me” -> luj -> variant_calling.
- 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.
- 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)
Expect a directory named gatk_haplotypecaller_output as output directory containing the vcf output files.