Calculates base frequency statistics across reference positions from BAM.
meta:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end
bam:file
A list of BAM or CRAM files
*.{bam,cram}
bai:file
List of BAM/CRAM index files
*.{bai,csi}
minqfile:file
File with individual quality score thresholds
*
depth_sample
*.depthSample:file
Distribution of sequencing depths
*.depthSample
depth_global
*.depthGlobal:file
*.depthGlobal
qs
*.qs:file
Distribution of scores
*.qs
pos
*.pos.gz:file
Various types of depth statistics (depending on value for -dumpCounts)
*.pos.gz
counts
*.counts.gz:file
Various types of statistics (related to pos.gz)
*.counts.gz
icounts
*.icnts.gz:file
Internal format for dumping binary single chrs. Useful for ANGSD contamination
*.icnts.gz
versions
versions.yml:file
File containing software versions
versions.yml
ANGSD: Analysis of next generation Sequencing Data
