10. RedDog pipeline outputs
d-j-e edited this page Oct 27, 2015
·
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If a reference FASTA file is provided in the config file, the following outputs are produced:
``` BAM files and indexes 'bam' subfolder .bam, .bam.bai VCF files* 'vcf' subfolder _q30.vcf Run statistics - summary^ Output folder _AllStats.txt Run statistics by replicon^ Output folder __RepStats.txt SNP allele matrix (0% cons) Output folder __alleles_var.csv SNP allele matrix^ (95% cons) Output folder __alleles_var_cons0.95.csv SNP difference matrix** Output folder __SNP_diff.nxs Concatenated SNPs Output folder __alleles.mfasta Tree (concatenated SNPs) Output folder __alleles.tree Outgroups Output folder __outgroup.txt *** Consensus Warning Output folder __cns_warning.txt **** Run Report Output folder _run_report.txt Sequence List Output folder sequence_list.txt ```
If a reference Genbank file is provided instead of a FASTA reference in the config file, the following outputs are also produced:
``` Percentage cover by gene^ Output folder _CoverMatrix.csv Depth by gene Output folder _DepthMatrix.csv Gene Presence/Absence Output folder _PresenceAbsence.csv SNP consequences outputs^ Output folder __alleles_var_cons0.95_consequences.txt, __alleles_var_cons0.95.gbk ```
NOTES:
\* optional output includes \\_hets.vcf if 'HetsVCF' set to ‘True’ \*\* optional output only generated if ‘DifferenceMatrix’ set to ‘True’ \*\*\* outgroup.txt will only be generated if there are any outgroups called for a replicon set. \*\*\*\* cns\_warning.txt only generated if SAMTools fails to generate a consensus sequence for an isolate (happens on the very odd occasion with smaller replicons, _e.g._ plasmids).
If the allele conservation is set to something other than 0.95, this will be reflected in the file names (where applicable)
For further information on those output files with a '^' above, see [Understanding the Output](https://github.com/katholt/RedDog/wiki/15.-Understanding-the-%28more-complex%29-Output)
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