The adam view
command implements some of the functionality of samtools view
, specifically the -f, -F, -c, and -o
options, in an optionally distributed fashion.
CalculateDepth (accessible as the command 'depth' through the CLI) takes two arguments, an Read file and a VCF (or equivalent) file, and calculates the number of reads (the 'depth') from the Read file which overlap each of the variants given by the VCF.
This set of classes executes a plugin along with the associated input location.
Reads in the tagStrings field of every record, and prints out the set of unique tags found in those fields along with the number of records that have each particular tag.
WigFix2Bed (accessible as the command "wigfix2bed" through the CLI) takes fixed wiggle file and converts it to a BED formatted file.