lumpyexpress - Automated breakpoint detection for standard
analyses
- -B FILE
- full BAM or CRAM file(s) (comma separated) (required)
- -S FILE
- split reads BAM file(s) (comma separated)
- -D FILE
- discordant reads BAM files(s) (comma separated)
- -R FILE
- indexed reference genome fasta file (recommended for CRAMs)
- -d FILE
- bedpe file of depths (comma separated and prefixed by sample:) e.g
sample_x:/path/to/sample_x.bedpe,sample_y:/path/to/sample_y.bedpe
- -o FILE
- output file [fullBam.bam.vcf]
- -x FILE
- BED file to exclude
- -P
- output probability curves for each variant
- -m INT
- minimum sample weight for a call [4]
-r FLOAT trim threshold [0]
- -T DIR
- temp directory [./output_prefix.XXXXXXXXXXXX]
- -k
- keep temporary files
- -K FILE
- path to lumpyexpress.config file
- (default: same directory as lumpyexpress)
- -v
- verbose
- -h
- show this message
Error: -B is required
This manpage was written by Andreas Tille for the Debian
distribution and
can be used for any other usage of the program.