Description of Output
By default, all output files stored into module-specific subdirectories within the output/ directory. However, each module in the pipeline includes an parameter (--output_dir) for the user to define the output directory.
Click on a tab below for details on output for each module …
| Subdirectory | Output Files | Description of Files |
|---|---|---|
abra | *.abra.log | number of reads before and after realignment for quality; WES only |
alfred | *.alfred.qc.[json.gz / summary.txt / txt.gz] | in-depth quality evaluation genome-wide alignment metrics of final BAM |
fastqc | *_fastqc.[html / zip] | in-depth quality evaluation on a per base and per sequence manner |
finalBams | *.final.[bam / bai] | final preprocessed BAM and index for downstream analysis |
laneMergedFastqs | *.merged.fastq.gz | concatenated FASTQs; lane split only |
trimmomatic | *.trimmomatic.log | number of reads before and after trimming for quality |
| Output File | Description of File |
|---|---|
*.deepvariant.germline.snp.indel.[vcf.gz / tbi] | germline SNP and InDel VCF |
*.fastngsadmix.23.[qopt / log] | per patient estimated admixture proportions |
The main output is found in the somatic/consensus output directory, where each sample has a subdirectoy with the following files:
| Output File | Description of File |
|---|---|
*.hq.union.consensus.somatic.snv.txt.gz | consensus SNV table |
*.hq.union.consensus.somatic.indel.txt.gz | consensus InDel table |
*.hq.union.consensus.somatic.cnv.bed | consensus CNV BED |
*.hq.union.consensus.somatic.sv.bedpe | consensus SV BEDPE |
*.hq.union.consensus.somatic.sv.intersection.plot.pdf | intersection of SV caller consensus |
Additional per-tool subdirectories included in the base output/somatic output directory:
| Subdirectory | Description of Files |
|---|---|
battenberg | native output of Battenberg |
conpair | native output of Conpair |
delly | native output of DELLY2 |
facets | native output of FACETS |
igcaller | native output of IgCaller |
manta | native output of Manta |
mutect | native output of Mutect2 |
sexOfSamples | sample sex estimation using alleleCount |
strelka | native output of Strelka2 |
svaba | native output of SvABA |
telomerecat | native output of Telomerecat |
telomereHunter | native output of TelomereHunter |
varscan | native output of VarScan2 |