Location and description of results files in GMS pipelines
The following example files were obtained from a complete run of the demonstration analysis of 12 lanes of Illumina (2x100bp) data generated for HCC1395 RNA and genomic DNA. The following therefore assumes an analysis generated with the processing-profiles specified in the demonstration build (18177dd5eca44514a47f367d9804e17a). Different processing-profiles may result in some files being missing and other files being added. Differences in input data (e.g. exome vs WGS data) may also influence what files are found in particular builds.
Each file below is an example from a single build of a model of the indicated type (reference-alignment, rna-seq, etc.). If you have multiple builds for a single model you would often use the last succeeded build. Refer to the tutorial for instructions on how to list models, builds, processing-profiles, etc. Note that many of the file paths below contain model, build and system IDs. These paths are examples only and these values will be different in your system.
all output from Illumina Infinium genotype array processing: /opt/gms/PEL8970/fs/PEL8970/info/model_data/2891230328/build911bed7cd98041748c7a62ab57942f73/2889981253.original
only genotype results from array analysis: /opt/gms/PEL8970/fs/PEL8970/info/model_data/2891230328/build911bed7cd98041748c7a62ab57942f73/2889981253.genotype
only copy number results: /opt/gms/PEL8970/fs/PEL8970/info/model_data/2891230328/build911bed7cd98041748c7a62ab57942f73/2889981253.copynumber
alignment BAM, flagstat report, picard metrics, etc.: /opt/gms/PEL8970/fs/PEL8970/info/model_data/2891325882/build5e8a09b77033494c8cc48873714e96e6/alignments/*
germline snv variant calls (vcf format): /opt/gms/PEL8970/fs/PEL8970/info/model_data/2891325882/build5e8a09b77033494c8cc48873714e96e6/variants/snvs.detailed.vcf.gz
germline indel variant calls (vcf format): /opt/gms/PEL8970/fs/PEL8970/info/model_data/2891325882/build5e8a09b77033494c8cc48873714e96e6/variants/indels.detailed.vcf.gz
germline snvs and indels - annotated against the transcriptome (custom TGI annotator): /opt/gms/PEL8970/fs/PEL8970/info/model_data/2891325882/build5e8a09b77033494c8cc48873714e96e6/variants/filtered.variants.post_annotation
alignment BAM and flagstat report: /opt/gms/PEL8970/fs/PEL8970/info/model_data/2891371548/build9e683f5b4b724a98a1ec2fc622c1d43a/alignments/*
detailed alignment statistics: /opt/gms/PEL8970/fs/PEL8970/info/model_data/2891371548/build9e683f5b4b724a98a1ec2fc622c1d43a/alignment_stats/*
detailed bam quality assessment results (fastqc, bam-error-rate, picard metrics, etc.): /opt/gms/PEL8970/fs/PEL8970/info/model_data/2891371548/build9e683f5b4b724a98a1ec2fc622c1d43a/bam-qc/*
gene and isoform expression output from Cufflinks: /opt/gms/PEL8970/fs/PEL8970/info/model_data/2891371548/build9e683f5b4b724a98a1ec2fc622c1d43a/expression/*
exon splicing results constructed from tophat junctions.bed file: /opt/gms/PEL8970/fs/PEL8970/info/model_data/2891371548/build9e683f5b4b724a98a1ec2fc622c1d43a/junctions/* observed.junctions.anno.NCBI-human.ensembl-67_37l_v2.tsv - splice junction expression values NCBI-human.ensembl-67_37l_v2.Junction.TranscriptExpression.tsv - transcript expression calculated from junctions NCBI-human.ensembl-67_37l_v2.Junction.GeneExpression.tsv - gene expression calculated from junctions
additional picard rna-seq metrics: /opt/gms/PEL8970/fs/PEL8970/info/model_data/2891371548/build9e683f5b4b724a98a1ec2fc622c1d43a/metrics/*
snv, indel, and sv calls (after filtering and converging of multiple callers) broken down by tiers: /opt/gms/PEL8970/fs/PEL8970/info/model_data/2891454547/build7b94706c62c2496ba63c167e53980f74/effects/*
high priority annotated somatic SNVs and InDels (in annotation format): /opt/gms/PEL8970/fs/PEL8970/info/model_data/2891454547/build7b94706c62c2496ba63c167e53980f74/effects/snvs.hq.tier1.rsid.v1.annotated.top /opt/gms/PEL8970/fs/PEL8970/info/model_data/2891454547/build7b94706c62c2496ba63c167e53980f74/effects/indels.hq.tier1.v1.annotated.top
high priority annotated SVs (in pair bed format): /opt/gms/PEL8970/fs/PEL8970/info/model_data/2891454547/build7b94706c62c2496ba63c167e53980f74/effects/svs.hq.annotated
all somatic SNVs in VCF format: /opt/gms/PEL8970/fs/PEL8970/info/model_data/2891454547/build7b94706c62c2496ba63c167e53980f74/variants/snvs.annotated.vcf.gz
all somatic InDels in VCF format: /opt/gms/PEL8970/fs/PEL8970/info/model_data/2891454547/build7b94706c62c2496ba63c167e53980f74/variants/indels.detailed.vcf.gz
all somatic CNVs (10 kb windows, tumor vs normal): /opt/gms/PEL8970/fs/PEL8970/info/model_data/2891454547/build7b94706c62c2496ba63c167e53980f74/variants/cnvs.hq
raw output from individual SNV, InDel, CNV, and SV callers (pre- and post- converging): /opt/gms/PEL8970/fs/PEL8970/info/model_data/2891454547/build7b94706c62c2496ba63c167e53980f74/variants/snv/ /opt/gms/PEL8970/fs/PEL8970/info/model_data/2891454547/build7b94706c62c2496ba63c167e53980f74/variants/indel/ /opt/gms/PEL8970/fs/PEL8970/info/model_data/2891454547/build7b94706c62c2496ba63c167e53980f74/variants/cnv/ /opt/gms/PEL8970/fs/PEL8970/info/model_data/2891454547/build7b94706c62c2496ba63c167e53980f74/variants/sv/
differential expression output from cuffdiff: /opt/gms/PEL8970/fs/PEL8970/info/model_data/abeb5a3cddb94374afffd617684fa49a/build1e98a9eaa90b4d5eac75e4904e4bb34e/differential_expression/*
output from cummeRbund: /opt/gms/PEL8970/fs/PEL8970/info/model_data/abeb5a3cddb94374afffd617684fa49a/build1e98a9eaa90b4d5eac75e4904e4bb34e/summarize_differential_expression/*
output from cuffcompare: /opt/gms/PEL8970/fs/PEL8970/info/model_data/abeb5a3cddb94374afffd617684fa49a/build1e98a9eaa90b4d5eac75e4904e4bb34e/transcript_convergence/
clonality plots (inference of clonal architecture and tumor purity): /opt/gms/PEL8970/fs/PEL8970/info/model_data/18177dd5eca44514a47f367d9804e17a/build8fad89994c77498b81caab3164976deb/TST1/clonality/*
single sample (tumor and normal) CNV plots /opt/gms/PEL8970/fs/PEL8970/info/model_data/18177dd5eca44514a47f367d9804e17a/build8fad89994c77498b81caab3164976deb/TST1/cnv/single_bam_cnv/
somatic CNV genes, digital karyotypes, chromosome-by-chromosome plots, etc: /opt/gms/PEL8970/fs/PEL8970/info/model_data/18177dd5eca44514a47f367d9804e17a/build8fad89994c77498b81caab3164976deb/TST1/cnv/cnview/*
CNV segments called by cnv-hmm: /opt/gms/PEL8970/fs/PEL8970/info/model_data/18177dd5eca44514a47f367d9804e17a/build8fad89994c77498b81caab3164976deb/TST1/clonality/cnaseq.cnvhmm
Automatically generated IGV sessions: /opt/gms/PEL8970/fs/PEL8970/info/model_data/18177dd5eca44514a47f367d9804e17a/build8fad89994c77498b81caab3164976deb/TST1/igv/*
WGS, Exome, and WGS+Exome annotated SNVs and InDels: /opt/gms/PEL8970/fs/PEL8970/info/model_data/18177dd5eca44514a47f367d9804e17a/build8fad89994c77498b81caab3164976deb/TST1/snv/* /opt/gms/PEL8970/fs/PEL8970/info/model_data/18177dd5eca44514a47f367d9804e17a/build8fad89994c77498b81caab3164976deb/TST1/indel/*
summary of QC results and med-seq inputs: /opt/gms/PEL8970/fs/PEL8970/info/model_data/18177dd5eca44514a47f367d9804e17a/build8fad89994c77498b81caab3164976deb/TST1/input/*
mutation diagrams (aka lollipop plots) for SNVs and InDels compared to COSMIC data: /opt/gms/PEL8970/fs/PEL8970/info/model_data/18177dd5eca44514a47f367d9804e17a/build8fad89994c77498b81caab3164976deb/TST1/mutation_diagrams/*
mutation rate, mutation spectrum, and mutation spectrum sequence context plots: /opt/gms/PEL8970/fs/PEL8970/info/model_data/18177dd5eca44514a47f367d9804e17a/build8fad89994c77498b81caab3164976deb/TST1/mutation-spectrum/
post-processed and annotated expression and differential expression results: /opt/gms/PEL8970/fs/PEL8970/info/model_data/18177dd5eca44514a47f367d9804e17a/build8fad89994c77498b81caab3164976deb/TST1/rnaseq/*
integration of WGS, Exome and RNA-seq data for SNV calls: /opt/gms/PEL8970/fs/PEL8970/info/model_data/18177dd5eca44514a47f367d9804e17a/build8fad89994c77498b81caab3164976deb/TST1/snv/wgs/summary/*
final SNV variant expression summary: /opt/gms/PEL8970/fs/PEL8970/info/model_data/18177dd5eca44514a47f367d9804e17a/build8fad89994c77498b81caab3164976deb/TST1/snv/wgs/summary/VariantExpressionSummary.tsv
DGIDB results - druggable mutation and gene analysis: Found throughout the results in directories named $input_genes.dgidb
candidate coding SV fusions and pairoscope plots for DNA fusion events: /opt/gms/PEL8970/fs/PEL8970/info/model_data/18177dd5eca44514a47f367d9804e17a/build8fad89994c77498b81caab3164976deb/TST1/sv/
comparison and summary of variant callers calling each SNV and InDel: /opt/gms/PEL8970/fs/PEL8970/info/model_data/18177dd5eca44514a47f367d9804e17a/build8fad89994c77498b81caab3164976deb/TST1/variant_source_callers/