b/tMSI-CAST (blood/tissue MSI Caller Adjusted with Sequence duplicaTes), an NGS-based composite MSI detection method that has a two-mode caller compatible with both tissue and plasma samples and does not require matched normal samples.
Version 0.10 Usage: msicast [options]
dedup_only perform duplication removal only. deletion-ratio MSI calling under the deletion-ratio mode. kld MSI calling under the kld mode.
-- inbam (-i) input BAM file -- outprefix (-o) prefix for a series of output files
-c coverage threshold for msi analysis, default=20 -b threads number for parallel computing, default=1 -y output microsatellite only, 0: no; 1: yes, default=0
take pre-deduplication BAMs as input and perform duplication removal by a proprietary majority-voting strategy.
If you have any questions, please contact one or more of the following folks: Beifang Niu bniu@sccas.cn Xinyin Han hanxinyin@cnic.cn