Realign reads mapped with BWA to elongated reference genome
Input
Name (Type)
Description
Pattern
meta (map)
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
bam (file)
BAM/SAM file
*.{bam,sam}
meta2 (map)
Groovy Map containing reference information
e.g. [ id:'test' ]
fasta (file)
Input elongated genome fasta
meta3 (map)
Groovy Map containing reference information
e.g. [ id:'test' ]
elongation_factor (integer)
The elongation factor used when running circulargenerator, i.e. the number of bases that the ends of the target chromosome in the reference genome was elongated by
Output
Name (Type)
Description
Pattern
meta (map)
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
