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btMSI-CAST

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.

Installation

b/tMSI-CAST is written in Perl. Directly download the entire directory and run msicast.pl to perform MSI dectection on a single test sample. No extra compilation is required.

Usage

Version 0.10 Usage: perl msicast.pl [options]

Options

-database <string> the directory that contains baseline databases.
-bam <string> the path of input BAM file.
-flank <int> spanning reads are defined as fully covering the coordinates of the microsatellite in reference plus flank bp in both 5’ and 3’ directions, default=2.
-num <int> the minimum allele supporting reads post-deduplication, default=2.
-minsize <int> minimum family size consdiered during deduplication, default=1.
-quality <int> minimum mapping quality, default=1.
-mode <string> available modes are 'DelRatio' and 'KLD', default=DelRatio.
-outdir <string> output directory.
-prefix <string> prefix for output files.

Example

An example command to run MSI detection on a single pre-deduplication BAM is:

perl $0 -database <database> -bam `bam` -flank 2 -num 2 -minsize 1 -quality 1 -mode DelRatio -outdir MSI -prefix `prefix`

The program takes a pre-deduplication BAM as input, perform realignment, duplication removal, call loci-level MSI status and sample-level MSI status.

Output files include:

  1. prefix.result.txt Each entry contains spanning reads information (readID, microsatellite sequence, read sequence, CIGAR and loci name) from the input BAM file.

  2. prefix.DUP.txt Each row contains the loci name, reference name, aligned starting position, insert size, lengths of each members pertaining to a family.

  3. prefix.stat.txt Each row represents info. of all fragments covering a locus, including DeletionRatios/KLD score, dup-ratios, and allele length offsets compared to the germline allele and corresponding frequencies.

  4. prefix.result.txt One line sample-level MSI calling results.

Contact

We can be reached by: Lili Zhao, zhao.lili@genecast.com.cn; Hongyu Xie, xie.hongyu@genecast.com.cn