diff --git a/tools/sniffles/sniffles.xml b/tools/sniffles/sniffles.xml index a6bf7c3a40f..3e207726f47 100644 --- a/tools/sniffles/sniffles.xml +++ b/tools/sniffles/sniffles.xml @@ -160,21 +160,22 @@ General ------- -+---------------------------+-----------------------------------------------------------------------+ -| Parameter | Description | -+===========================+=======================================================================+ -| Minimum Support | Minimum number of reads supporting a SV to be reported. Default:auto | -+---------------------------+-----------------------------------------------------------------------+ -| Maximum Number of Splits | Maximum number of split segments per kb a read is aligned at before | -| | it is ignored. Default: 7 | -+---------------------------+-----------------------------------------------------------------------+ -| Minimum SV Length | Minimum length of SV to be reported. Default: 50bp | -+---------------------------+-----------------------------------------------------------------------+ -| Minimum Mapping Quality | Minimum mapping quality of alignment to be taken into account. | -| | Default: 20 | -+---------------------------+-----------------------------------------------------------------------+ -| Minimum alignment length | Reads with less length aligned will be ignored. Default 100 | -+---------------------------+-----------------------------------------------------------------------+ ++----------------------------+-------------------------------------------------------------------------+ +| Parameter | Description | ++============================+=========================================================================+ +| Minimum Support | Minimum number of reads supporting a SV to be reported. Default:auto | ++----------------------------+-------------------------------------------------------------------------+ +| Maximum Number of Splits | Maximum number of split segments per kb a read is aligned at before | +| | it is ignored. Default: 7 | ++----------------------------+-------------------------------------------------------------------------+ +| Minimum SV Length | Minimum length of SV to be reported. Default: 50bp | ++----------------------------+-------------------------------------------------------------------------+ +| Minimum Mapping Quality | Minimum mapping quality of alignment to be taken into account. | +| | Default: 20 | ++----------------------------+-------------------------------------------------------------------------+ +| Minimum alignment length | Reads with less length aligned will be ignored. Default 100 | ++----------------------------+-------------------------------------------------------------------------+ + @@ -182,25 +183,27 @@ Clustering Options ------------------ -+----------------------------------------+-----------------------------------------------------------------------+ -| Parameter | Description | -+========================================+=======================================================================+ -| Cluster bin size | Initial cluster bin size. Default 100 | -+----------------------------------------+-----------------------------------------------------------------------+ -| Cluster Multiplier | Multiplier for SV start position standard deviation criterion in | -| | cluster merging [2.5] | -+----------------------------------------+-----------------------------------------------------------------------+ ++---------------------+------------------------------------------------------------------------+ +| Parameter | Description | ++=====================+========================================================================+ +| Cluster bin size | Initial cluster bin size. Default 100 | ++---------------------+------------------------------------------------------------------------+ +| Cluster Multiplier | Multiplier for SV start position standard deviation criterion in | +| | cluster merging [2.5] | ++---------------------+------------------------------------------------------------------------+ + + Advanced Options ---------------- -+----------------------------------------+------------------------------------------------------------------------------+ -| Parameter | Description | -+========================================+==============================================================================+ -| Mosaic | Set Sniffles run mode to detect rare, somatic and mosaic SVs (default: False)| -+----------------------------------------+------------------------------------------------------------------------------+ ++-------------+--------------------------------------------------------------------------------+ +| Parameter | Description | ++=============+================================================================================+ +| Mosaic | Set Sniffles run mode to detect rare, somatic and mosaic SVs (default: False)| ++-------------+--------------------------------------------------------------------------------+ ----