Output files

Final outputs

Each successful run writes two files to --out:

wisp.bed.gz
wisp.bed.gz.tbi

The population count mask is bgzip-compressed and indexed with tabix -p bed. Use --output-prefix to choose a different filename stem; .bed.gz is always appended.

BED columns

The mask starts with two comment-prefixed header lines:

#wisp_mask_metadata  {"columns":["chrom","start","end","GBR","YRI"],...}
#chrom  start  end  GBR  YRI

Data rows contain:

chrom

Chromosome or contig name.

start

0-based BED start coordinate.

end

0-based BED end coordinate, exclusive.

population columns

Number of samples in each population with depth greater than or equal to --min-dp over the interval.

Adjacent bases with identical population counts are collapsed. Intervals where all counts are zero are omitted.

Metadata

The #wisp_mask_metadata line is JSON. It includes:

  • wisp_mask_version

  • format

  • columns

  • coordinate_system

  • zero_count_intervals_omitted

  • min_dp

  • sample_count

  • populations

  • population_columns

  • population_sample_counts

  • input paths such as samples_path, popfile, all_sites_vcf, and mask_bed when applicable

  • variants_vcf, threshold_sources, and variant_vcf_threshold_estimates when --variants-vcf is used in BAM/CRAM mode

Sparse interpretation

The mask is sparse by design. A missing interval means zero passing samples in every population — not that the interval was skipped or that counts are unknown.

When --variants-vcf excludes an indel, structural variant, breakend, or multi-nucleotide polymorphism span in BAM/CRAM mode, that span is removed from all sample pass BEDs. In the final sparse BED, this is represented the same way as any other all-zero region: no data row is written for the span.

Intermediate files

When --keep-work is set, BAM/CRAM mode retains files like:

mask.3col.bed
mask.3col.sorted.merged.bed
<sample>.d<min-dp>.quantized.bed.gz
<sample>.d<min-dp>.quantized.bed.gz.csi
<sample>.d<min-dp>.mosdepth.summary.txt
<sample>.d<min-dp>.mosdepth.global.dist.txt
<sample>.d<min-dp>.mosdepth.stderr.log
<sample>.d<min-dp>.pass.bed
<sample>.d<min-dp>.pass.targets.bed
variants_vcf.excluded.raw.bed
variants_vcf.excluded.sorted.merged.bed
<sample>.d<min-dp>.pass.variants.bed
<sample>.d<min-dp>.pass.targets.variants.bed
cohort.d<min-dp>.multiinter.tsv
cohort.d<min-dp>.population_count_quantized.bed

The variants_vcf.* and *.variants.bed files are present only when --variants-vcf finds non-SNP exclusion intervals.

VCF mode retains the uncompressed population count mask in the work directory.