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Error: -B is required #379

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khalidanaveed opened this issue May 24, 2022 · 0 comments
Open

Error: -B is required #379

khalidanaveed opened this issue May 24, 2022 · 0 comments

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@khalidanaveed
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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?

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