output

Output files

For each sample, V-pipe produces several output files that are located in the corresponding sample-specific directory. First, the alignment file and consensus sequences are located in the alignments and references subdirectories, respectively. Second, output files containing SNVs and viral haplotypes are located in the variants subdirectories.

Below, we provide an example of relevant output files and their locations, following the same structure as in the getting-started section. The output files for the two patient samples will be located in the following subdirectories:

working_directory
├─references
│  └───HXB2.fasta
└─samples
  ├──patient1
  │   ├──20100113
  │   │   ├──alignments
  │   │   |  └──REF_aln.bam
  │   │   ├──references
  |   |   |  ├──ref_ambig.fasta
  |   |   |  └──ref_majority.fasta
  |   |   └──variants
  |   |      ├──SNVs
  |   |      |  └──snvs.vcf
  |   |      └──global
  |   |         └──contigs_stage_c.fasta
  │   └──20110202
  │      ├──alignments
  │       |  └──REF_aln.bam
  │       ├──references
  |       |  ├──ref_ambig.fasta
  |       |  └──ref_majority.fasta
  |       └──variants
  |          ├──SNVs
  |          |  └──snvs.vcf
  |          └──global
  |             └──contigs_stage_c.fasta         
  └──patient2
          ├──alignments
          |  └──REF_aln.bam
          ├──references
          |  ├──ref_ambig.fasta
          |  └──ref_majority.fasta
          └──variants
             ├──SNVs
             |  └──snvs.vcf
             └──global
                └──contigs_stage_c.fasta

In addition, V-pipe generates a csv file containg the frequencies of all minor alleles that differ from the consensus among analysed samples. This ouput file is located in the variants subdirectory

working_directory
└─variants
  └───minority_variants.tsv