Skip to content

Latest commit

 

History

History
77 lines (64 loc) · 7.23 KB

output.md

File metadata and controls

77 lines (64 loc) · 7.23 KB
Raw

Understand outputs file

The directory structure for the clusterV results is as below:

.
├── ${OUTPUT_DIR}
│   ├── consensus                   # output of clusterV
│   │   ├── all_report.tsv          # drug resistance report for found subtypes
│   │   ├── all_info.tsv            # statistics for all found subtypes, with abundance information
│   │   ├── id_1_report.tsv         # HIVDB report for subtype 1
│   │   ├── id_1_report.json        # [raw HIVDB](https://hivdb.stanford.edu/page/release-notes/#json.output) report output for subtype 1
│   │   ├── id_1.fasta              # consensus for subtype 1
│   │   ├── id_1                    # data directory for subtype 1
│   │   │   ├── id_1.bam            # all read alignment in bam file for subtype 1
│   │   │   ├── id_1_cs.bam         # single consensus alignment for subtype 1
│   │   │   ├── id_1_cs.vcf         # all variants in consensus for subtype 1
│   │   │   ├── id_1_low_af.vcf     # low AF variants in subtypes but not in consensus for subtype 1
│   │   │   └── ...
│   │   ├── id_2                    # data directory for subtype 2
│   │   │   └── ...
│   │   └── ...
│   ├── clustering                      # working files for clusterV algorithm
│   │   ├── all_clusters_info.tsv       # clustering results, subtypes, abundance, and files location information 
│   │   ├── 1                           # first iteration
│   │   │   └── 1.tagged.bam  		# bam file with subtype labeling after 1st iteration                 
│   │   │   └── 1.tagged.tag1.bam  	# subtype 1 after 1st iteration                 
│   │   │   └── 1.tagged.tag2.bam  	# subtype 2 after 1st iteration                 
│   │   │   └── ...                 
│   │   ├── 1_1                     # subtype after first iteration 
│   │   │   └── ...                 
│   │   └── ...             
│   ├── ${SAMPLE_ID}_f.bam          # BAM file after initalize filtering
│   └── ...                 
└── ...

drug resistance report for found subtypes

all drug resistance report is available at all_report.tsv

column description
gene Gene name from HIVDB
drugClass Drug class name from HIVDB
drugName Drug name from HIVDB
drugScore Drug score from HIVDB
resistanceLevel Drug resistance level from HIVDB
subtype_ori Subtype raw ID when running clustering
subtype Subtype ID
abundance Subtype's abundance
is_in_consensus Whether the drug resistance mutation found in consensus (1 if found in subtype, 0 if found in low AF set)
VAF variants AF in subtype
mutationPos mutation genome position in HIV reference
mutation mutation name
mutationScore mutation sscore in HIVDB
mutationType mutation type in HIVDB
comments mutation comments from HIVDB

statistics for all found subtypes, with abundance information

all subtype information is available at all_info.tsv

column description
_idx subtype ID
_vcf raw VCF for subtypes during clustering
_bam raw BAM for the subtype during clustering
_out_dir working directory for the subtype during clustering
_sample_id sample ID
_sample_idx raw index for the subtype
is_check_clustering checking status for subtypes, whether try splitting in this subtype
percentage subtype's abundance
_v_info:coverage;snp_c;indel_c;median_af;af1;af2;af3 subtype's coverage, # of SNP, # of INDEL, the median of AF, # of raw AF in [0, 0.3], # of raw AF in [0.3, 0.7], # of raw AF in [0.7, 1.0]