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PapenfussLab / gridss

GRIDSS: the Genomic Rearrangement IDentification Software Suite
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What is "ldsv" in the help? #43

Closed tseemann closed 7 years ago

tseemann commented 8 years ago 
USAGE: Idsv [options]

Calls structural variations from one or more SAM/BAM input files.
Version: 0.11.7
d-cameron commented 8 years ago

GRIDSS is technically a software suite, but currently released version includes only the IDSV (IDentification of Structural Variant) entry point. I'll update the documentation in the next release which will modularise the pipeline into independently usable components (SAM tag rehydration, DP identification, split read identification, assembly, variant calling) using only spec-defined SAM tags in intermediate files.

Hopefully this will encourage alternate implementation of various steps (eg Pindel split read identification, or CLEVER discordant read pair identification) that can be swapped out to generate new pipelines. One can dream.

d-cameron commented 7 years ago

overhaul of command line entry points. namespace is now "gridss"