Add readme

Author: edolzhenko

README.md

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+# TRGT-instability
+
+TRGT-instability is an add-tool for [TRGT](https://github.com/PacificBiosciences/trgt/)
+designed to quantify instability of each repeat allele.
+
+## Availability
+
+The latest binary can be found in the release page.
+
+## Usage example
+
+The tool can be run like so:
+
+```bash
+./trgt-instability --repeats repeats.bed --spanning-reads sample.trgt.sorted.bam 
+```
+
+where
+
+- `repeats.bed` is the BED file with repeat definitions; it must be the same file
+as the one used to run TRGT,
+- `sample.trgt.sorted.bam` is the BAM file generated by TRGT; it must be sorted
+and indexed.
+
+The output will look like this:
+
+```tsv
+trid allele motif motif_counts expansion_rate contraction_rate model_params
+FMR1 1      CGG   84,93,94,94,95,95,95,96,97,97,99,100,100,101,101,101,104,104,107,108,109,113,116,126  0.06 0.05  0.96:0.01:0.61:0.80
+```
+
+where:
+
+- `trid` is the tandem repeat identifier from `repeats.bed`
+- `allele` is the allele index
+- `motif` is the motif profiled
+- `motif_count` is the number of motifs identified in each read
+- `expansion_rate` is the estimated expansion rate (see below)
+- `contraction_rate` is the estimated contraction rate (see below)
+- `model_params` are the estimated parameters of the instability model
+
+The expansion and contraction rate parameters are motivated by a simple
+model where mosaicism can occur due to slippage during DNA replication.
+An expansion rate of 0.01 means that an allele consisting of 100 motifs
+is expected to have a single motif expansion event during replication.