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Firepony can be run with the following command line arguments:
firepony -r <reference FASTA file> -s <SNP database file> -o <output table file> <input alignment file>
-rspecifies the path to the reference file (in uncompressed FASTA format, equivalent to GATK option
-sspecifies the path to the SNP database file (in BCF or VCF format, equivalent to GATK option
Firepony will load an index for the reference file if it exists, which enables on-demand loading of reference sequences as the SNP database is loaded.
For example, the following GATK command line:
java -Xmx8g GenomeAnalysisTK-3.4.jar \ -T BaseRecalibrator \ -I NA12878D_HiSeqX_R1.deduplicated.bam \ -R /store/ref/hs37d5.fa \ -knownSites /store/dbsnp/dbsnp_138.b37.vcf \ -o recal_data.table
would be replaced by the following Firepony command line:
firepony \ -r /store/ref/hs37d5.fa -s /store/dbsnp/dbsnp_138.b37.vcf \ -o recal_data.table NA12878D_HiSeqX_R1.deduplicated.bam
Additional command line options are described in the help output for firepony invoked by
Note that it is recommended to use the BCF format rather than VCF for SNP databases when running Firepony. Both generate the same results, but loading BCF files is much more efficient.
At the moment, Firepony only supports recalibrating Illumina reads with the default GATK BQSR parameters, listed below in BQSR table format. Expanding the parameter set as well as the number of supported instruments will be done based on user feedback.
#:GATKTable:Arguments:Recalibration argument collection values used in this run Argument Value binary_tag_name null covariate ReadGroupCovariate,QualityScoreCovariate,ContextCovariate,CycleCovariate default_platform null deletions_default_quality 45 force_platform null indels_context_size 3 insertions_default_quality 45 low_quality_tail 2 maximum_cycle_value 500 mismatches_context_size 2 mismatches_default_quality -1 no_standard_covs false quantizing_levels 16 recalibration_report null run_without_dbsnp false solid_nocall_strategy THROW_EXCEPTION solid_recal_mode SET_Q_ZERO