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Config_Indel_Realign
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#!/bin/bash
# This config runs indel realignment steps only. Please see "Config" file for full pipeline.
# More complete information on how to fill out
# this Config file can be found at:
# https://github.com/MorrellLAB/sequence_handling/wiki/Configuration
# Where are we storing the output files?
# Final directory is ${OUT_DIR}/Name_of_Handler
OUT_DIR=
# Name this project
PROJECT=
# What email should we use for job notifications?
EMAIL=
# What encoding is used for quality values?
# Look at the FastQC files to determine
# the sequence encoding. Choose from:
# 'sanger', 'illumina'
# 'solexa', or 'phred'
QUAL_ENCODING=
# Sequencing platform technology
# What platform were the reads produced?
# Valid options are:
# CAPILLARY, LS454, ILLUMINA,
# SOLID, HELICOS, IONTORRENT
# ONT, and PACBIO
SEQ_PLATFORM=
# What reference genome are we using?
# Include the full file path.
REF_GEN=
# Is this organism barley?
# Choose from: "true" or "false"
BARLEY=
# Are you running the analysis on the Minnesota Supercomputing Institute (MSI)?
# Choose from: "true" or "false"
MSI=
# Are you submitting the job with qsub from PBS (Portable Batch System)
# Choose from: "true" or "false"
USE_PBS=
# Do the quality scores need to be adjusted for GATK? Default: false
# Change to true if you get errors from GATK like:
# "<Sample> appears to be using the wrong encoding for quality scores: we encountered an extremely high quality score"
FIX_QUALITY_SCORES=
# Where should Picard/GATK store temporary files?
# If you've encountered issues with running out of temp space
# with picard, you can optionally specify a temp directory
# Otherwise, leave blank
TMP=
############################################
######## Realigner_Target_Creator ########
############################################
# What are our Qsub settings for Realigner_Target_Creator?
# Below are the recommended settings
RTC_QSUB="mem=22gb,nodes=1:ppn=16,walltime=24:00:00"
# Where is the list of finished BAM files?
# To generate this list, use sample_list_generator.sh
# located at /sequence_handling/HelperScripts/sample_list_generator.sh
RTC_BAM_LIST=
############################################
######### Indel_Realigner #########
############################################
# What are our Qsub settings for Indel_Realigner?
# Below are the recommended settings
IR_QSUB="mem=22gb,nodes=1:ppn=16,walltime=24:00:00"
# Where is the list of finished BAM files?
# To generate this list, use sample_list_generator.sh
# located at /sequence_handling/HelperScripts/sample_list_generator.sh
IR_BAM_LIST=
# Where is the list of realigner targets files (.intervals)?
# To generate this list, use sample_list_generator.sh
# located at /sequence_handling/HelperScripts/sample_list_generator.sh
IR_TARGETS=
# IR_BAM_LIST and IR_TARGETS must have the same sample order.
# What is the LOD threshold above which the cleaner will clean?
# GATK default: 5.0, Barley: 3.0
LOD_THRESHOLD=3.0
# What is the percentage of mismatches at a locus to be considered having high entropy (0.0 < entropy <= 1.0)?
# GATK default: 0.15, Barley: 0.10
ENTROPY_THRESHOLD=0.10
############################################
########## Dependencies ##########
############################################
# This section defines installations to
# various dependencies for sequence_handling.
# If you are using the Minnesota Supercomputing Institute cluster
# then uncomment all 'module load' lines.
# Make sure you have access to all '_ML' modules.
# If you need to install a dependency from source,
# then uncomment the lines for the dependency and the
# 'export PATH=', and write the full path to the executable
# for the program. For example:
# PARALLEL=${HOME}/software/parallel-20151122/bin/parallel
# If you have a system-wide installation for a program, you can
# leave all lines commented out. sequence_handling will find
# system-wide installed programs automatically.
# Please visit https://github.com/MorrellLab/sequence_handling/wiki/Dependencies
# for information on version requirements and compatibility
if [[ "$MSI" == "true" ]] ; then
# Do we have GNU parallel installed
module load parallel/20190122
#PARALLEL=
#export PATH=${PARALLEL}:${PATH}
# Do we have Java installed?
module load java/openjdk-8_202
#JAVA=
#export PATH=${JAVA}:${PATH}
# What is the full file path for the GATK jar file?
# You need BOTH the jar file and the module
# NOTE: Indel realignment functionality is not in GATK v4. Please use GATK v3.
GATK_JAR=/panfs/roc/groups/9/morrellp/public/Software/GATK_ML_3.8.0/GenomeAnalysisTK.jar
module load gatk_ML/3.8.0
# What is the full file path for the Picard jar file?
PICARD_JAR=/home/morrellp/public/Software/picard_ML_2.20.2/picard.jar
fi