Calculates genome-wide sequencing coverage.
meta:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end
bam:file
Input BAM/CRAM file
*.{bam,cram}
bai:file
Index for BAM/CRAM file
*.{bai,crai}
bed:file
BED file with intersected intervals
*.{bed}
meta2:map
Groovy Map containing bed information e.g. [ id:‘test’ ]
fasta:file
Reference genome FASTA file
*.{fa,fasta}
global_txt
*.global.dist.txt:file
Text file with global cumulative coverage distribution
*.{global.dist.txt}
summary_txt
*.summary.txt:file
Text file with summary mean depths per chromosome and regions
*.{summary.txt}
regions_txt
*.region.dist.txt:file
Text file with region cumulative coverage distribution
*.{region.dist.txt}
per_base_d4
*.per-base.d4:file
D4 file with per-base coverage
*.{per-base.d4}
per_base_bed
*.per-base.bed.gz:file
BED file with per-base coverage
*.{per-base.bed.gz}
per_base_csi
*.per-base.bed.gz.csi:file
Index file for BED file with per-base coverage
*.{per-base.bed.gz.csi}
regions_bed
*.regions.bed.gz:file
BED file with per-region coverage
*.{regions.bed.gz}
regions_csi
*.regions.bed.gz.csi:file
Index file for BED file with per-region coverage
*.{regions.bed.gz.csi}
quantized_bed
*.quantized.bed.gz:file
BED file with binned coverage
*.{quantized.bed.gz}
quantized_csi
*.quantized.bed.gz.csi:file
Index file for BED file with binned coverage
*.{quantized.bed.gz.csi}
thresholds_bed
*.thresholds.bed.gz:file
BED file with the number of bases in each region that are covered at or above each threshold
*.{thresholds.bed.gz}
thresholds_csi
*.thresholds.bed.gz.csi:file
Index file for BED file with threshold coverage
*.{thresholds.bed.gz.csi}
versions
versions.yml:file
File containing software versions
versions.yml
Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing.
