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MACARON-GenMed-LabEx/LICENSE.txt MACARON-GenMed-LabEx/MACARON MACARON-GenMed-LabEx/MACARON_validate.sh MACARON-GenMed-LabEx/README.md MACARON-GenMed-LabEx/_config.yml MACARON-GenMed-LabEx/demo/MACARON_output.txt MACARON-GenMed-LabEx/demo/MACARON_validate.txt MACARON-GenMed-LabEx/demo/sub1.chr22_21349676-21349677.sample02.bam MACARON-GenMed-LabEx/demo/variants_of_interest.vcf MACARON-GenMed-LabEx/index.html |
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| diff -r 000000000000 -r c9636a827049 MACARON-GenMed-LabEx/LICENSE.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/MACARON-GenMed-LabEx/LICENSE.txt Wed Sep 12 08:45:03 2018 -0400 |
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| @@ -0,0 +1,64 @@ +GNU LESSER GENERAL PUBLIC LICENSE +Version 3, 29 June 2007 + +Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/> + +Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. + +This version of the GNU Lesser General Public License incorporates the terms and conditions of version 3 of the GNU General Public License, supplemented by the additional permissions listed below. +0. Additional Definitions. + +As used herein, “this License” refers to version 3 of the GNU Lesser General Public License, and the “GNU GPL” refers to version 3 of the GNU General Public License. + +"The Library" refers to a covered work governed by this License, other than an Application or a Combined Work as defined below. + +An “Application” is any work that makes use of an interface provided by the Library, but which is not otherwise based on the Library. Defining a subclass of a class defined by the Library is deemed a mode of using an interface provided by the Library. + +A “Combined Work” is a work produced by combining or linking an Application with the Library. The particular version of the Library with which the Combined Work was made is also called the “Linked Version”. + +The “Minimal Corresponding Source” for a Combined Work means the Corresponding Source for the Combined Work, excluding any source code for portions of the Combined Work that, considered in isolation, are based on the Application, and not on the Linked Version. + +The “Corresponding Application Code” for a Combined Work means the object code and/or source code for the Application, including any data and utility programs needed for reproducing the Combined Work from the Application, but excluding the System Libraries of the Combined Work. +1. 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Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns. + +Each version is given a distinguishing version number. If the Library as you received it specifies that a certain numbered version of the GNU Lesser General Public License “or any later version” applies to it, you have the option of following the terms and conditions either of that published version or of any later version published by the Free Software Foundation. If the Library as you received it does not specify a version number of the GNU Lesser General Public License, you may choose any version of the GNU Lesser General Public License ever published by the Free Software Foundation. + +If the Library as you received it specifies that a proxy can decide whether future versions of the GNU Lesser General Public License shall apply, that proxy's public statement of acceptance of any version is permanent authorization for you to choose that version for the Library. |
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| diff -r 000000000000 -r c9636a827049 MACARON-GenMed-LabEx/MACARON --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/MACARON-GenMed-LabEx/MACARON Wed Sep 12 08:45:03 2018 -0400 |
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| b'@@ -0,0 +1,560 @@\n+#!/usr/bin/python\n+\n+#alpha version 0.7 (05/09/18)\n+\n+"""\n+#Script to identify SNPs located within a genetic codon:\n+\n+Annotation of SNPs (including synonymous and non-synonymous variants) located within the same genetic codon requires attention. This idea conflicts with the annotations observed by traditional annotation software widely used now a days. While looking at the combined effect within the framework of genetic codon, we have new / altered codons that code for new amino acid that can be predicted by using this MACARON python script.\n+\n+#####------How to run quickly run MACARON-------\n+\n+# python MACARON -i yourinputfile.vcf\n+\n+# python MACARON -i /path/to/yourinputfile.vcf -o /path/to/MACARON_output.txt -f (INFO)_FIELD_HEADER --GATK /path/to/GenomeAnalysisTK.jar --HG_REF /path/to/hg.fasta --SNPEFF /path/to/snpeff.jar --SNPEFF_HG hg19 \n+\n+# python MACARON -i yourinputfile.vcf -o MACARON_output.txt --gatk4 (when using gatk versions >= 4.0)\n+\n+"""\n+\n+import sys, os, time\n+import itertools\n+import multiprocessing\n+import re\n+import subprocess\n+from argparse import ArgumentParser\n+\n+## GLOBAL VARIABLES (IMPORTANT: You can set the default values here)\n+GATK="/home/wuk/software/GenomeAnalysisTK.jar"\n+#GATK="/home/wuk/software/gatk-4.0.1.2/gatk-package-4.0.1.2-local.jar"\n+HG_REF="/home/wuk/Working/gnme_refrnces/Homo_sapiens_assembly19.fasta"\n+SNPEFF="/home/wuk/software/snpEff/snpEff.jar"\n+SNPEFF_HG="GRCh37.75" ## SnpEff human genome annotation database version\n+\n+## PRINTINGS, AESTHETICS\n+str_progress_list = ["\\tIndexing VCF file",\n+\t\t "\\tIdentifying SnpClusters",\n+\t\t "\\tExtracting SnpClusters",\n+\t\t "\\tAnnotating SnpClusters",\n+\t\t "\\tExcluding InDels",\n+\t\t "\\tGenerating a SnpCluster Table",\n+\t\t "\\tRe-annotating Codons",\n+\t\t "\\tRemoving SnpCluster if AA_Change_pcSNV == (AA1 or AA2)",\n+\t\t "\\tExtracting established SnpClusters - for which two (or three) SNPs are reference heterozygous (or non-reference homozygous)"]\n+header = ("\\n" +\n+\t "(###############)\\n" +\n+\t "@@@@ MACARON @@@@\\n" +\n+\t "(###############)\\n\\n" +\n+\t "Starting....\\n")\n+footer = "\\nMACARON Run Completed. Bon Courage with Analysis ...,,,!!!!\\n"\n+\n+def animate(keep_anim, idx):\n+\tc = "|/-\\\\"\n+\ti=0\n+\twhile keep_anim.is_set():\n+\t\ti += 1\n+\t\tsys.stdout.write("\\r>" + str_progress_list[idx] + ": " + c[i % len(c)] +"\\r")\n+\t\tsys.stdout.flush()\n+\t\ttime.sleep(0.1)\n+\tsys.stdout.write("\\r " + str_progress_list[idx] + ": Done!\\n")\n+def print_step(keep_anim, idx):\n+\tif not(ECO):\n+\t\tkeep_anim.set()\n+\t\tanim_thread = multiprocessing.Process(target=animate, args=(keep_anim, idx))\n+\t\tanim_thread.start()\n+\t\treturn anim_thread\n+\telse:\n+\t\tsys.stdout.write(">" + str_progress_list[idx] + ": in progress...\\r" )\n+\t\tsys.stdout.flush()\n+\t\treturn None\n+def end_print_step(keep_anim, anim_thread, idx):\n+\tif not(ECO):\n+\t\tkeep_anim.clear(); anim_thread.join()\n+\telse:\n+\t\tsys.stdout.write(" " + str_progress_list[idx] + ": Done!\t \\n")\n+\t\tsys.stdout.flush()\n+\n+\n+## CLASS DEFINITIONS \n+\t\t\n+class fileHandler:\n+\tdef __init__(self):\n+\t\tself.data = []; \n+\tdef open_file(self, readfl):\n+\t\tself.rfile = open(readfl, \'r\').readlines()\n+\t\treturn self.rfile\n+\tdef write_file(self, writefl):\n+\t\tself.wfile = open(writefl, \'w\')\n+\t\treturn self.wfile\n+\n+class SearchDB(fileHandler):\n+\tdef __init__(self):\n+\t\tself.data = [] \n+\t\tfrom collections import defaultdict\n+\t\tself.ident_ranges_HMBM = defaultdict(list)\n+\tdef Search_CODON(self, vcf_input, workdir, FIELDS):\n+\t\t"""\n+\t\tCalling SNPClusters\n+\t\t\n+\t\tUSAGE INSTRUCTIONS:\tFull path to the software directories should be set before compiling.\n+\t\t"""\n+\n+\t\t#######################\n+\t\tFld_Len = int(len(FIELDS.split(",")))\n+\t\tFldwithF = " ".join(["-F " + str(x) for x in FIELDS.split(",")])\n+\n+\t\t## Options compatible with GATK versions >= 4.0: add option --gatk4 when calling MACARON\n+\t\tif GATK4:\n+\t\t\tGATK_v, SNPeff_v = (" ", " -v ") if VERBOSE else (" --QUIET true --verbosity ERROR ", " ")\n+\t\t\tcmd0 = "java -Xmx12g -jar " + GATK + '..b' the same genetic codon)")\n+\tparser.add_argument("-i", "--infile", dest="INPUTFile",default=False, required=True, help="Full path of the input VCF file.")\n+\tparser.add_argument("-o", "--outfile", dest="OUTPUTFile",default="./MACARON_output.txt", required=False, help="Path of the output txt file (Default Output file: MACARON_output.txt)")\n+\tparser.add_argument("-f", "--fields", dest="Fields", default="QUAL", required=False, help=" Single field name or comma-seperated \',\' multiple field names can be given. Field name should be given according to the (INFO) field header of the input vcf file. Example: -f Func.refGene,ExonicFunc.refGene,Gene.refGene,1000g2015aug_all,ExAC_ALL,ExAC_EAS,clinvar_20161128,gnomAD_exome_ALL,gnomAD_genome_ALL,EFF,CSQ")\n+\tparser.add_argument("--GATK", dest="GATK_path", default=GATK, required=False, help="Indicate the full path to GATK jar file")\n+\tparser.add_argument("--HG_REF", dest="HG_REF_path", default=HG_REF, required=False, help="Indicate the full path to the reference genome fasta file")\n+\tparser.add_argument("--SNPEFF", dest="SNPEFF_path", default=SNPEFF, required=False, help="Indicate the full path to SnpEff jar file")\n+\tparser.add_argument("--SNPEFF_HG", dest="SNPEFF_HG_version", default=SNPEFF_HG, required=False, help="Indicate SnpEff human genome annotation database version")\n+\tparser.add_argument("--gatk4", dest="GATK4", default=False, required=False, action=\'store_true\', help="Add this option when using GATK versions >= 4.0")\n+\tparser.add_argument("-v", "--verbosity", dest="Verbosity", default=False, required=False, action=\'store_true\', help="Use to print verbosity (Mostly GATK/SNPEFF output)")\n+\tparser.add_argument("-c", "--eco_friendly", dest="ECO", default=False, required=False, action=\'store_true\', help="Save a thread, but you won\'t be able to stare at the fabulous animation while waiting ...")\n+\n+\t## Assign arguments to global variables\n+\targs = parser.parse_args()\n+\tFIELDS = args.Fields\n+\tGATK4 = args.GATK4\n+\tVERBOSE = args.Verbosity\n+\tGATK = args.GATK_path\n+\tHG_REF = args.HG_REF_path\n+\tSNPEFF = args.SNPEFF_path\n+\tSNPEFF_HG = args.SNPEFF_HG_version\n+\tECO = args.ECO\n+\n+\t## Inputs / Outputs path & names\n+\tINF = args.INPUTFile\n+\tOUTF = args.OUTPUTFile\n+\tTMPDIR = os.path.dirname(os.path.abspath(OUTF)) + "/macaron_tmp/"\n+\tsubprocess.check_output("mkdir -p " + TMPDIR, shell=True)\n+\n+\t########################\n+\t## MAIN PROCESS ##\n+\t########################\n+\tprint(header)\n+\t\n+\t## Check if global variables point to existing files:\n+\tINF_check = os.path.exists(INF)\n+\tGATK_check = os.path.exists(GATK)\n+\tHG_REF_check = os.path.exists(HG_REF)\n+\tSNPEFF_check = os.path.exists(SNPEFF)\n+\tSNPEFF_HG_non_empty = (SNPEFF_HG != "")\n+\tif not(INF_check and GATK_check and HG_REF_check and SNPEFF_check and SNPEFF_HG_non_empty):\n+\t\tprint(">ERROR : One or several global variable: \\n VCF={} > {}\\n GATK={} > {}\\n HG_REF={} > {}\\n SNPEFF={} > {}\\n SNPEFF_HG={} > {}\\n>Please correct and try again!".format(INF, INF_check, GATK, GATK_check, HG_REF, HG_REF_check, SNPEFF, SNPEFF_check, SNPEFF_HG, SNPEFF_HG_non_empty))\n+\t\tsys.exit(1)\n+\telse: ## If everything checks out, start MACARON\n+\t\t## Animation event initialization\n+\t\tkeep_anim = multiprocessing.Event()\n+\n+\t\t## 1)VARIANTS FILTERING, ANNOTATION (GATK,SNPEff)\n+\t\tclF1 = SearchDB().Search_CODON(INF, TMPDIR, FIELDS)\n+\t\t## 2)SEARCH MULTI-SNPS CODONS\n+\t\tthread = print_step(keep_anim, 6)\n+\t\tclF2 = SearchDB().TWO_VAR(TMPDIR)\n+\t\tclF3 = SearchDB().THREE_VAR(TMPDIR)\n+\t\tend_print_step(keep_anim, thread, 6)\n+\t\t## 3)CHECK IF SNPCLUSTERS IMPACT CODON\n+\t\tthread = print_step(keep_anim, 7)\n+\t\tclF4 = SearchDB().PARS_OUT_VAR(TMPDIR)\n+\t\tend_print_step(keep_anim, thread, 7)\n+\t\t## 4) EXTRACT SNPCLUSTERS (Keeping SnpCluster if >=1 sample is Ref-Heterozygous or nonRef-Homozygous)\n+\t\tthread = print_step(keep_anim, 8)\n+\t\tclF5 = SearchDB().ZYGO_PAIR(OUTF, TMPDIR, FIELDS)\n+\t\tend_print_step(keep_anim, thread, 8)\n+\t\tprint(footer)\n+\tsubprocess.check_output("rm -r " + TMPDIR, shell=True)\n' |
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| diff -r 000000000000 -r c9636a827049 MACARON-GenMed-LabEx/MACARON_validate.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/MACARON-GenMed-LabEx/MACARON_validate.sh Wed Sep 12 08:45:03 2018 -0400 |
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| @@ -0,0 +1,49 @@ +#!/bin/bash + +#sub1.chr22_21349676-21349677.sample02.bam + +bam=$1; +name=$(echo $bam | cut -d'.' -f1) +region=$(echo $bam | cut -d'.' -f2) +sample=$(echo $bam | cut -d'.' -f3) + +chr=$(echo $region | cut -d'_' -f1) +pos=$(echo $region | cut -d'_' -f2) + +beg=$(echo $pos | cut -d'-' -f1) +end=$(echo $pos | cut -d'-' -f2) + +#beg=$(($beg+50)) +#end=$((end-50)) + +#echo "name $name" +#echo "region $region" +#echo "sample $sample" + +echo "$name $chr:$beg-$end $sample" +echo "$name $chr:$beg-$end $sample" >> MACARON_validate.txt + +samtools view $bam | awk -v start=$beg -v stop=$end ' +{ + pos=$4; + if(pos < start){ + cstart=1+start-pos; + cstop=1+stop-pos; + print cstart"."cstop"."$10; + } +}' > tmp + +while read line; +do + cb=$(echo $line | cut -d'.' -f1); + ce=$(echo $line | cut -d'.' -f2); + seq=$(echo $line | cut -d'.' -f3); + echo $seq | cut -c$cb-$ce; +done <tmp | sort | uniq -c | sort -n >> MACARON_validate.txt +rm tmp + + + + +exit 0 + |
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| diff -r 000000000000 -r c9636a827049 MACARON-GenMed-LabEx/README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/MACARON-GenMed-LabEx/README.md Wed Sep 12 08:45:03 2018 -0400 |
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| b'@@ -0,0 +1,286 @@\n+MACARON User Guide\n+================\n+\n+# Table of Contents\n+\n+[//]: # (BEGIN automated TOC section, any edits will be overwritten on next source refresh)\n+\n+* [Introduction](#introduction)\n+* [Installation](#installation)\n+ * [Operating System Guidelines](#operating-system-guidelines)\n+ * [Runtime Pre-requisite](#runtime-pre-requisite)\n+ * [Software Dependencies](#software-dependencies)\n+ * [Downloading the Source Code](#downloading-the-source-code)\n+ * [Contents of the Folder MACARON_GenMed](#contents-of-the-folder-macaron_genmed)\n+* [Running the MACARON](#running-the-macaron)\n+ * [Input Requirements](#input-requirements)\n+ * [Default Options](#default-options)\n+ * [demo Folder](#demo-folder)\n+ * [Advanced Options](#advanced-options)\n+* [MACARON Reporting Format](#macaron-reporting-format)\n+* [Validating SNVs Existed on the Same Reads](#validating-snvs-existed-on-the-same-reads)\n+* [References](#references)\n+* [Citation](#citation)\n+\n+[//]: # (END automated TOC section, any edits will be overwritten on next source refresh)\n+\n+# Introduction\n+\n+MACARON (Multi-bAse Codon-Associated variant Re-annotatiON) is a python framework to identify and re-annotate multi-base affected codons in whole genome/exome sequence data. Starting from a standard VCF file, MACARON identifies, re-annotates and predicts the amino acid change resulting from multiple single nucleotide variants (SNVs) within the same genetic codon. \n+\n+The information below includes how to install and run MACARON to filter a list of variant records (from VCF file) called by any existing SNP-based variant caller to identify SNVs with the same genetic codon and correct their corresponding amino acid change.\n+\n+See latest [News](https://github.com/waqasuddinkhan/MACARON-GenMed-LabEx/wiki/News???) and [Updates](https://github.com/waqasuddinkhan/MACARON-GenMed-LabEx/wiki#updates) on [MACARON-GenMed-LabEx Wiki page](https://github.com/waqasuddinkhan/MACARON-GenMed-LabEx/wiki).\n+\n+# Installation\n+\n+### Operating System Guidelines\n+\n+MACARON is know to run on LINUX UBUNTU 16.04 LTS. However, MACARON can be run on any other LINUX version.\n+\n+### Runtime Pre-requisite\n+\n+__1.__ MACARON is executable in __PYTHON v2.7 or later__. If the user has multiple PYTHON versions, please make sure that your running environment is set to the required version of PYTHON.\n+\n+__2.__ Check your __JAVA__ version as MACARON is tested with:\n+\n+ java -version\n+ openjdk version __"1.8.0_151"__\n+ OpenJDK Runtime Environment (build 1.8.0_151-8u151-b12-0ubuntu0.16.04.2-b12)\n+ OpenJDK 64-Bit Server VM (build 25.151-b12, mixed mode)\n+\n+### Software Dependencies\n+\n+Before running MACARON, please make sure that following software are installed properly:\n+\n+__1.__ __Genome-Analysis Toolkit__ (https://software.broadinstitute.org/gatk/download/).\n+\n+__2.__ __SnpEff__ (tested with __v4.3__ (build 2017-05-05 18:41). However, MACARON can also run with any older or newer version (http://snpeff.sourceforge.net/download.html).\n+\n+__3.__ __SAMTools__ (tested with version __0.1.19__), however any version can be used.\n+\n+__4.__ __Human Reference Genome__: Depends on user\xe2\x80\x99s input.\n+\n+__5.__ __SnpEff\xe2\x80\x99s Human Annotation Database__: Depends on user\xe2\x80\x99s input.\n+\n+For __1__ and __2__, as long as they are compatible with JAVA, MACARON has no issues.\n+\n+### Downloading the Source Code\n+\n+The most prefered way to use the lastest version of MACARON is:\n+\n+ git clone https://github.com/waqasuddinkhan/MACARON-GenMed-LabEx.git\n+\n+or download the ZIP folder.\n+\n+MACARON source code can also be downloaded from http://www.genmed.fr/images/publications/data/MACARON_GenMed.zip\n+\n+After acquiring a release distribution of the source code, the build procedure is to unpack the zip file:\n+\n+ unzip MACARON_GenMed.zip\n+\n+### Contents of the folder MACARON_GenMed\n+\n+* *MACARON* \xe2\x80\x93 The MACARON python code\n+* *MACARON_validate.sh* \xe2\x80\x93 a BASH-shell script to validat'..b'+8 | FILTER | Filter (PASS) tag\n+9 | SIFT_pred | Functional effect prediction of SNV on protien\n+10 | [SAMPLE NAME].GT | Genotype of samples as base conventions as well as binary conventions\n+11 | Protein_coding_EFF | Functional Effect of Variant on protein\n+12 | AA-Change | Amino acid change by individual SNV\n+13 | REF-codon | Reference Codon\n+14 | ALT-codon | Alternate Codon\n+15 | ALT-codon_merge-2VAR | A new codon formed by the combination of two Alt-codons (pcSNV codon; see [MACARON](https://academic.oup.com/bioinformatics/advance-article-abstract/doi/10.1093/bioinformatics/bty382/4992149?redirectedFrom=fulltext))\n+16 | AA-Change-2VAR | Re-annotated amino acid formed by pcSNV codon\n+17 | ALT-codon_merge-3VAR | A new codon formed by the combination of three Alt-codons\n+18 | AA-Change-3VAR | Re-annotated amino acid formed by the combination of three Alt-codons\n+\n+# Validating SNVs Existed on the Same Reads\n+\n+**NB: You do not need to run this step if you already used phased VCF file to run MACARON**\n+\n+To confirm the existence of multi-SNVs within the same genetic codon, an accessory BASH-shell script [MACARON_validate.sh](MACARON_validate.sh) calculates the read count information of affected bases. This script requires as an input subset of BAM files (should be the same that used to generate the input VCF file) covering 50 bps over each SnpCluster.\n+\n+Subset of any BAM file can be generated by using the following command:\n+\n+`\n+samtools view \xe2\x80\x93hb \xe2\x80\x93L sub1.bed sample02.bam > sub1.chr22_21349676-21349677.sample02.bam\n+`\n+\n+In this case, our big BAM file `sample02.bam` (not provided here, obviously!!!) is subsetted as `sub1.chr22_21349676-21349677.sample02.bam` (see [demo](demo) folder) for the position `chr22:21349676`. The naming format of output BAM file should be the same. The `sub1.bed` file has 1 tab-seperated line:\n+\n+`chr22 21349676`\n+\n+representing the first position of SnpCluster (SNV1 only).\n+ \n+Once subset BAM file(s) are generated, run MACARON_validate.sh:\n+\n+`MACARON_validate.sh sub1.chr22_21349676-21349677.sample02.bam`\n+\n+This will generate an output text file (`MACARON_validate.txt`) allowing the user for further analysis.\n+\n+ sub1 chr22:21349676-21349677 sample02\n+ 1 AA\n+ 1 T\n+ 11 AT\n+ 14 TC\n+\n+See [MACARON-GenMed-LabEx Wiki page](https://github.com/waqasuddinkhan/MACARON-GenMed-LabEx/wiki) for more details, and interpretations of the [demo](demo) data.\n+\n+# References\n+\n+__1.__ [Van der Auwera G.A., et al. (2013) From FastQ Data to High-Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline, Curr Protoc Bioinformatics, 43:11.10.1-11.10.33](https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/0471250953.bi1110s43).\n+\n+__2.__ [Cingolani, P., et al. (2012) A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3, Fly, 6, 80-92](https://www.tandfonline.com/doi/full/10.4161/fly.19695).\n+\n+__3.__ [McLaren, W., et al. (2010) Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor, Bioinformatics, 26, 2069-2070](https://academic.oup.com/bioinformatics/article/26/16/2069/217748).\n+\n+__4.__ [Wang, K., Li, M. and Hakonarson, H. (2010) ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data, Nucleic Acids Res, 38, e164](https://academic.oup.com/nar/article/38/16/e164/1749458).\n+\n+# Citation\n+\n+If you use [MACARON](https://academic.oup.com/bioinformatics/advance-article-abstract/doi/10.1093/bioinformatics/bty382/4992149?redirectedFrom=fulltext) in your research, please cite:\n+\n+*Khan W. et al. MACARON: a python framework to identify and re-annotate multi-base affected codons in whole genome/exome sequence data, Bioinformatics 2018*\n+\n+*CONTACT: david-alexandre.tregouet@inserm.fr; waqasnayab@gmail.com*\n+\n+*VERSION: 0.7*\n+*VERSION DATE: September 5, 2018*\n' |
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| diff -r 000000000000 -r c9636a827049 MACARON-GenMed-LabEx/_config.yml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/MACARON-GenMed-LabEx/_config.yml Wed Sep 12 08:45:03 2018 -0400 |
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| @@ -0,0 +1,15 @@ +plugins: + - jekyll-seo-tag + +title: macaron +username: waqasuddinkhan +url: https://github.com/waqasuddinkhan/MACARON-GenMed-LabEx + +webmaster_verifications: + google: 1234 + bing: 1234 + alexa: 1234 + yandex: 1234 + baidu: 1234 + +theme: jekyll-theme-cayman |
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| diff -r 000000000000 -r c9636a827049 MACARON-GenMed-LabEx/demo/MACARON_output.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/MACARON-GenMed-LabEx/demo/MACARON_output.txt Wed Sep 12 08:45:03 2018 -0400 |
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| @@ -0,0 +1,5 @@ +CHROM POS ID REF ALT Gene_Name QUAL sample01.GT sample02.GT sample03.GT sample01.GT sample02.GT sample03.GT Protein_coding_Gene_Name AA-Change REF-codon ALT-codon ALT-codon_merge-2VAR AA-Change-2VAR ALT-codon_merge-3VAR AA-Change-3VAR +chr22 21349676 rs412470 T A LZTR1 423.0 T/T T/A T/T 0/0 0/1 0/0 MISSENSE S92T Tct Act ATt I . . +chr22 21349677 rs376419 C T LZTR1 423.0 C/C C/T C/C 0/0 0/1 0/0 MISSENSE S92F tCt tTt . I . . +chr22 23247169 rs527511481 T G IGLJ3 719.0 T/T T/G T/T 0/0 0/1 0/0 MISSENSE W39G Tgg Ggg GTg V . . +chr22 23247170 rs540954398 G T IGLJ3 716.0 G/G G/T G/G 0/0 0/1 0/0 MISSENSE W39L tGg tTg . V . . |
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| diff -r 000000000000 -r c9636a827049 MACARON-GenMed-LabEx/demo/MACARON_validate.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/MACARON-GenMed-LabEx/demo/MACARON_validate.txt Wed Sep 12 08:45:03 2018 -0400 |
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| @@ -0,0 +1,5 @@ +sub1 chr22:21349676-21349677 sample02 + 1 AA + 1 T + 11 AT + 14 TC |
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| diff -r 000000000000 -r c9636a827049 MACARON-GenMed-LabEx/demo/sub1.chr22_21349676-21349677.sample02.bam |
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| Binary file MACARON-GenMed-LabEx/demo/sub1.chr22_21349676-21349677.sample02.bam has changed |
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| diff -r 000000000000 -r c9636a827049 MACARON-GenMed-LabEx/demo/variants_of_interest.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/MACARON-GenMed-LabEx/demo/variants_of_interest.vcf Wed Sep 12 08:45:03 2018 -0400 |
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| b'@@ -0,0 +1,395 @@\n+##fileformat=VCFv4.2\n+##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">\n+##FILTER=<ID=LowQual,Description="Low quality">\n+##FILTER=<ID=VQSRTrancheINDEL99.00to99.90,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: -16.0255 <= x < -0.8001">\n+##FILTER=<ID=VQSRTrancheINDEL99.90to100.00+,Description="Truth sensitivity tranche level for INDEL model at VQS Lod < -37813.1681">\n+##FILTER=<ID=VQSRTrancheINDEL99.90to100.00,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: -37813.1681 <= x < -16.0255">\n+##FILTER=<ID=VQSRTrancheSNP99.90to100.00+,Description="Truth sensitivity tranche level for SNP model at VQS Lod < -123623.5614">\n+##FILTER=<ID=VQSRTrancheSNP99.90to100.00,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -123623.5614 <= x < -2.5203">\n+##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">\n+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">\n+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">\n+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n+##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">\n+##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another">\n+##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group">\n+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">\n+##FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)">\n+##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher\'s Exact Test to detect strand bias.">\n+##GVCFBlock0-1=minGQ=0(inclusive),maxGQ=1(exclusive)\n+##GVCFBlock1-2=minGQ=1(inclusive),maxGQ=2(exclusive)\n+##GVCFBlock10-11=minGQ=10(inclusive),maxGQ=11(exclusive)\n+##GVCFBlock11-12=minGQ=11(inclusive),maxGQ=12(exclusive)\n+##GVCFBlock12-13=minGQ=12(inclusive),maxGQ=13(exclusive)\n+##GVCFBlock13-14=minGQ=13(inclusive),maxGQ=14(exclusive)\n+##GVCFBlock14-15=minGQ=14(inclusive),maxGQ=15(exclusive)\n+##GVCFBlock15-16=minGQ=15(inclusive),maxGQ=16(exclusive)\n+##GVCFBlock16-17=minGQ=16(inclusive),maxGQ=17(exclusive)\n+##GVCFBlock17-18=minGQ=17(inclusive),maxGQ=18(exclusive)\n+##GVCFBlock18-19=minGQ=18(inclusive),maxGQ=19(exclusive)\n+##GVCFBlock19-20=minGQ=19(inclusive),maxGQ=20(exclusive)\n+##GVCFBlock2-3=minGQ=2(inclusive),maxGQ=3(exclusive)\n+##GVCFBlock20-21=minGQ=20(inclusive),maxGQ=21(exclusive)\n+##GVCFBlock21-22=minGQ=21(inclusive),maxGQ=22(exclusive)\n+##GVCFBlock22-23=minGQ=22(inclusive),maxGQ=23(exclusive)\n+##GVCFBlock23-24=minGQ=23(inclusive),maxGQ=24(exclusive)\n+##GVCFBlock24-25=minGQ=24(inclusive),maxGQ=25(exclusive)\n+##GVCFBlock25-26=minGQ=25(inclusive),maxGQ=26(exclusive)\n+##GVCFBlock26-27=minGQ=26(inclusive),maxGQ=27(exclusive)\n+##GVCFBlock27-28=minGQ=27(inclusive),maxGQ=28(exclusive)\n+##GVCFBlock28-29=minGQ=28(inclusive),maxGQ=29(exclusive)\n+##GVCFBlock29-30=minGQ=29(inclusive),maxGQ=30(exclusive)\n+##GVCFBlock3-4=minGQ=3(inclusive),maxGQ=4(exclusive)\n+##GVCFBlock30-31=minGQ=30(inclusive),maxGQ=31(exclusive)\n+##GVCFBlock31-32=minGQ=31(inclusive),maxGQ=32(exclusive)\n+##GVCFBlock32-33=minGQ=32(inclusive),maxGQ=33(exclusive)\n+##GVCFBlock33-34=minGQ=33(inclusive),maxGQ=34(exclusive)\n+##GVCFBlock34-35=minGQ=34(inclusive),maxGQ=35(exclusive)\n+##GVCFBlock35-36=minGQ=35(inclusive),maxGQ=36(exclusive)\n+##GVCFBlock36-37=minGQ=36(inclusive),maxGQ=37(exclusive)\n+##GVCFBlock37-38=minGQ=37(inclusive),maxGQ=3'..b'=.;GWAVA_region_score=.;GWAVA_tss_score=.;GWAVA_unmatched_score=.;ALLELE_END;ANNOVAR_DATE=2016-02-01;CADD13_RawScore=-2.133468;CADD13_PHRED=0.001;ALLELE_END\tGT:AD:DP:GQ:PGT:PID:PL\t0/0:.:53:99:.:.:0,120,255\t0/1:.:28:99:.:.:255,0,255\t0/0:.:40:0:.:.:0,0,255\n+chr22\t23247170\trs540954398\tG\tT\t716\tPASS\tAC=1;AF=0.167;AN=6;BaseQRankSum=1.73;ClippingRankSum=0.00;DB;DP=122;ExcessHet=3.0103;FS=9.423;MLEAC=1;MLEAF=0.167;MQ=49.47;MQRankSum=-4.088e+00;NEGATIVE_TRAIN_SITE;QD=24.70;ReadPosRankSum=-3.910e-01;SOR=1.911;VQSLOD=-2.392e+00;culprit=SOR;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGg/tTg|W39L|49|IGLJ3|IG_J_gene|CODING|ENST00000390324|1|T|WARNING_TRANSCRIPT_INCOMPLETE),UPSTREAM(MODIFIER||1342||105|IGLC3|IG_C_gene|CODING|ENST00000390325||T|WARNING_TRANSCRIPT_NO_START_CODON),DOWNSTREAM(MODIFIER||3553||105|IGLC2|IG_C_gene|CODING|ENST00000390323||T|WARNING_TRANSCRIPT_NO_START_CODON);ANNOVAR_DATE=2016-02-01;Func.refGene=intergenic;Gene.refGene=IGLL5,RSPH14;GeneDetail.refGene=dist\\x3d9157\\x3bdist\\x3d154423;ExonicFunc.refGene=.;AAChange.refGene=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;InterVar(automated)=.;PVS1=.;PS1=.;PS2=.;PS3=.;PS4=.;PM1=.;PM2=.;PM3=.;PM4=.;PM5=.;PM6=.;PP1=.;PP2=.;PP3=.;PP4=.;PP5=.;BA1=.;BS1=.;BS2=.;BS3=.;BS4=.;BP1=.;BP2=.;BP3=.;BP4=.;BP5=.;BP6=.;BP7=.;esp6500siv2_ea=.;esp6500siv2_all=.;ExAC_ALL=0.1225;ExAC_AFR=0.1998;ExAC_AMR=0.0548;ExAC_EAS=0.1777;ExAC_FIN=0.1607;ExAC_NFE=0.1143;ExAC_OTH=0.1207;ExAC_SAS=0.1145;gnomAD_exome_ALL=0.0906;gnomAD_exome_AFR=0.1949;gnomAD_exome_AMR=0.0726;gnomAD_exome_ASJ=0.0615;gnomAD_exome_EAS=0.2403;gnomAD_exome_FIN=0.0928;gnomAD_exome_NFE=0.0729;gnomAD_exome_OTH=0.0885;gnomAD_exome_SAS=0.0669;gnomAD_genome_ALL=.;gnomAD_genome_AFR=.;gnomAD_genome_AMR=.;gnomAD_genome_ASJ=.;gnomAD_genome_EAS=.;gnomAD_genome_FIN=.;gnomAD_genome_NFE=.;gnomAD_genome_OTH=.;1000g2015aug_all=0.103035;MCAP=.;REVEL=.;GWAVA_region_score=.;GWAVA_tss_score=.;GWAVA_unmatched_score=.;ALLELE_END;ANNOVAR_DATE=2016-02-01;CADD13_RawScore=-1.839588;CADD13_PHRED=0.002;ALLELE_END\tGT:AD:DP:GQ:PGT:PID:PL\t0/0:.:53:99:.:.:0,120,255\t0/1:.:29:99:.:.:255,0,255\t0/0:.:40:15:.:.:0,15,255\n' 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| diff -r 000000000000 -r c9636a827049 MACARON-GenMed-LabEx/index.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/MACARON-GenMed-LabEx/index.html Wed Sep 12 08:45:03 2018 -0400 |
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| @@ -0,0 +1,6 @@ +<html> + <head> + {% include index.html %} + {macaron waqas} + </head> +</html> |