Description of output
The most important outputs are merged_muts_drm_annotated.csv, a comma-separated-value file
that can be conveniently opened in any spreadsheet program, and report.md/report.pdf,
a mostly comprehensive report of the sample written in markdown format and that
includes the columns from merged_muts_drm_annotated.csv. Other files are discussed below.
The columns are, in order,
gene, can be RT (reverse transcriptase), protease, or integrase (GagPolTF is included inmerged_muts_drm_annotated.csv, but not in the final report) for HIV, or NS3, NS5A, NS5B for HCV (other genes are not in the final report)pos, a number indicating the position on that gene where a mutation with respect to consensus B (for HIV) or H77 isolate (for HCV) sequence was observed,mut, the amino acid found at that position, if different from consensus B,freq, the frequency at which it was found,category, the classification of the mutation according to HIVdb (for HIV) or to the list of RAS mutations (for HCV).
The report also includes a rough estimate of the subtype for the analyzed sample. This is done by aligning a subset of reads to sequences representative of different subtypes and choosing the best match. The distribution of best matches gives an idea of the most likely subtype for the sample. For HIV, a better approach is to take the sample consensus and run HIV BLAST (see below).
Other output
Sample consensus
A consensus sequence for the sample is found in cns_final.fasta. This can be
used, for example, to run
HIV BLAST
from Los Alamos HIV Database.
Main alignment file
The alignment of (at most) 200,000 reads to the sample consensus is
in file hq_2_cons_sorted.bam. One can explore this alignment, for example,
with the command
samtools tview hq_2_cons_sorted.bam cns_final.fasta