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Welcome to the iMSAT wiki page!

This page is for installing and trouble shooting the iMSAT program.

I've recently (2016-01-25) updated the script to v1.2. Sorry for not providing updates sooner.

iMSAT requires the following:
1) a modified fasta formatted input file - the current version needs the input file to be a formatted as follows;

contig_1 <tab> sequence
contig_2 <tab> sequence
contig_3 <tab> sequence
...
contig_n <tab> sequence</tab></tab></tab></tab>

2) a modified vcf formatted polymorphism report file generated using samtools (all of the header information needs to be removed so that the file starts with the first polymorphic site).

The user then specifies the minimum number of repeat units, and the minimum distance between polymorphic sites.

Some post analysis clean-up is required, currently each microsatellite is counted twice, once as AT and a second time as TA. I'm working on it.

Let me know if this helps.

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Project Members:

• jeremycandersen (admin)