Explain Output¶
All results generated by lohhlamod are stored in the directory specified
by the --outdir flag.
Output Files¶
The output directory contains filtered alignments, the final statistical results, and intermediate data for visualization.
-
LOH result(
*.loh.res.tsv): The primary output file containing LOH calls and copy number estimates. Each row corresponds to a specific HLA allele pair. -
Filtered alignment(
*.filt.bam): BAM files filtered by the minimum allowed mismatch events (controlled by the--min-ecntoption). These files represent the high-confidence reads used for the final LOH detection. -
Intermediate objects(
*.rds): R-serialized data files containing intermediate data table objects for each allele.
Deep dive analyses
These RDS files are highly valuable. While lohhlaplot command utilizes
them to generate diagnostic plots (see Visulization page),
you can also load them directly into an R session to perform custom
downstream analyses, inspect raw statistics not available in the
primary result, or create your own interactive visualizations.
LOH result schema¶
The main result file provides a detailed breakdown of copy number (CN) estimates and the statistical strength of the LOH call.
| Column | Description |
|---|---|
| HLA_A1_CN | Estimated copy number for Allele 1. Upper and lower bounds are provided as _Upper and _Lower. |
| HLA_A2_CN | Estimated copy number for Allele 2. |
| Pct_CN_Diff_Supporting_Bins | % of bins showing a significant CN difference between Allele 1 and Allele 2. |
| HLA_A[1/2]_Median_LogR | Median log-ratio of Tumor vs. Normal coverage across all bins for the respective allele. |
| HLA_A[1/2]_MM_Median_LogR | Median log-ratio of Tumor vs. Normal coverage specifically at mismatch sites. |
| MM_LogR_Paired_Pvalue | P-value from a paired test comparing the log-ratio difference between the two alleles at mismatch sites. This corresponds to the PVal legacy metric in HLALOH. |
| Median_BAF | Median B-Allele Frequency (BAF) across all mismatch sites. |
| NUM_MM | Total number of mismatch positions identified between the two alleles. |
| NUM_Bins | Total number of 150bp (default) bins across the pairwise alignment. |
| NUM_MM_Bins | Total number of bins that contain at least one mismatch site. |
| Pct_A[1/2]_Loss_Supporting_Bins | % of bins showing a significant copy number loss for the respective allele. |
| HLAGene | The HLA locus (e.g., HLA-A, HLA-B, HLA-C). |
| HLA_A[1/2] | The specific nomenclature of the two alleles being compared. |