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arq5x / lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery
MIT License
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Error: -B is required #379

Open khalidanaveed opened 2 years ago

khalidanaveed commented 2 years ago

biit@biit-HP-Z400-Workstation:~/Downloads/lumpy-sv$ lumpyexpress -v Sourcing executables from /usr/local/bin/lumpyexpress.config ...

Checking for required python modules (/usr/bin/python)...

usage: lumpyexpress [options]

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

how to recover it?