added readme

Author: AvrahamKahan123

README.md

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+
+############################################################################################
+############################################################################################
+#### Copyright (c) 2017, Broad Institute
+#### Redistribution and use in source and binary forms, with or
+without
+#### modification, are permitted provided that the following
+conditions are
+#### met:
+
+####     Redistributions of source code must retain the above
+         copyright
+####     notice, this list of conditions and the following disclaimer.
+
+####     Redistributions in binary form must reproduce the above
+         copyright
+####     notice, this list of conditions and the following disclaimer
+         in
+####     the documentation and/or other materials provided with the
+####     distribution.
+
+####     Neither the name of the Broad Institute nor the names of its
+####     contributors may be used to endorse or promote products
+####     derived
+####     from this software without specific prior written permission.
+
+#### THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+     CONTRIBUTORS
+#### "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+#### LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
+     FOR
+#### A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
+     COPYRIGHT
+#### HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
+     INCIDENTAL,
+#### SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+#### LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+     USE,
+#### DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+     ANY
+#### THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR
+     TORT
+#### (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE
+     USE
+#### OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+     DAMAGE.
+############################################################################################
+############################################################################################
+
+######################################################################################################
+####### MSMuTect - Calling somatic MS indels
+######################################################################################################
+####### For details on the implementation 
+####### see YE  Maruvka, Mouw K,  et al, Analysis of somatic
+microsatellite indels identifies driver events in human tumors 
+####### Nat. Biotechnology (2017) DOI: *****
+#
+# Written by Yosef E. Maruvka and Gad Getz
+#
+#############################################
+
+
+
+
+
+It needs the following tools:
+1. Bedtools
+2. Samtools
+3. Bowtie2
+4. R 2.15.3 (or similar but bot R 3.)
+5. Python-2.7 .
+6. PHOBOS. It should be obtained from
+http://www.ruhr-uni-bochum.de/ecoevo/cm/cm_phobos.htm and be placed
+under the bin/ folder.
+
+The command needed to be run from the MSMuTect directory (the needed
+tools are in bin/ folder and the data is in reference/ folder)
+
+MSMuTect has two step:
+
+1. Allele calling per sample 
+
+sh bin/shell_for_all.sh sample_ID BAM_file_PATH BAM_file_ID 
+
+e.g.:
+sh bin/shell_for_all.sh Normal data/ Normal.bam 
+sh bin/shell_for_all.sh Tumor  data/ Tumor.bam 
+
+
+2. MS_indel calling (per pair)
+
+sh bin/ms_indel_calling.sh 
+
+This step needs a file (space delimited, called Pairs2.ls in the
+MSMuTect folder) that specifies the pairs for calling mutations. 
+E.g.
+Tumor Normal
+
+The output MS indels will be under the Tumor folder (e.g. Tumor).
+The format is a tab delimited maf_like file for every motif.
+
+The "Decision" column for every candidat indel is:
+
+1  - passed the threshold 
+0  - did not pass the threshold
+-1 - filtered due to the normal sample have two alleles with one
+having a to low fraction
+-2 - filtered due to the normal sample have more than two alleles
+-3 - filtered due to not passing the KS-test
+
+The current reference loci are on hg19 and includes the exome territory
+only.
+
+
+For comments suggstions or errors please contact
+maruvka@broadinstitute.org 
+