lumpyexpress1

Usage

Options

-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