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Config.conf
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Config.conf
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[OPTIONS]
# Threads are a standin for processes now.
Threads = 16
snpRate = 0.2
minCov = 1
# SNP Filtering options.
LengthOf5pTrim = 15
Min3pQuality = 30
Min3pLength = 30
phred = 64
# Number of CPUs
processes = 16
# Java Memory Allocation
# Suggested to be large for files larger than 30 gb.
# Minimum should probably be set equal to max.
maxheap = 30g
minheap = 8g
[PIPELINE]
# RUN2_Filter
# All of the options are run at once now keep on.
# If you don't want an option to run change the trim, length, or quality in Options.
# Change to 0 if you want to not run that option.
# Compressed still exists to unzip files if they're gzipped.
FivePrimeFilter = 1
ThreePrimeFilter= 1
PairedEnd = 1
Compressed = 0
# RUN4_PrepBAM
SortSam = 1
ReadGroups = 1
MarkDups = 1
# RUN5_GATK2
RealignTC = 1
IndelRealign = 1
HaplotypeCall = 1
# RUN6_VEP
[VEP]
version = 82
# species = brachypodium_distachyon
species = bdist
# Not functional yet don't use.
conv2GTF = 0
# Variant Effect Predictor 78 and up will take gffs.
# It's all lies, no cache database creation for now.
# Switch on to 1, if the cache database for your genome isn't in the VEP directory.
makeCDB = 0
# VEP is functional.
callvar = 1
# Filter VCF via homozygous, heterozygous, or missing (hom,het,miss)
# To exclude use ^hom or ^het. For further info, view bcftools view.
filter = 1
type = hom
[GATK]
gtmode = DISCOVERY
outmode = EMIT_ALL_SITES
[PATHS]
#samtools = /nfs4shares/bioinfosw/installs_current/samtools/samtools
samtools = /home/clizarraga/usr/bin/samtools
bowtie2 = /nfs4shares/bioinfosw/installs_current/bowtie2-2.1.0/bowtie2
#bcftools = /nfs4shares/bioinfosw/installs_current/samtools/bcftools/bcftools
bcftools = /home/clizarraga/usr/bin/bcftools
# picard = /nfs4shares/bioinfosw/installs_current/picard/dist/picard.jar
picard = /home/clizarraga/usr/local/picard-tools-1.141/picard.jar
4gatk = /home/clizarraga/usr/local/gatk/GenomeAnalysisTK.jar
java = /home/clizarraga/usr/bin/java8
# Reference Genome
reference = /shares/tmockler_share/clizarraga/Brachypodium_distachyon/Phytozome/v3.1/assembly/Bdistachyon_314_v3.0.hardmasked.fa
# Bowtie2 Indices (stub to use)
# indices = /shares/tmockler_share/clizarraga/bdaccessions/Ref/Brachypodium_distachyon.mainGenome.masked.fasta
indices = /shares/tmockler_share/clizarraga/Brachypodium_distachyon/Phytozome/v3.1/assembly/indices/Bdistachyon_314_v3.0.hardmasked
# GATK2 uses Picard Tools fasta dictionary.
# fadict = /shares/tmockler_share/clizarraga/bdaccessions/Ref/Brachypodium_distachyon.mainGenome.masked.fasta.dict
fadict = /shares/tmockler_share/clizarraga/Brachypodium_distachyon/Phytozome/v3.1/assembly/Bdistachyon_314_v3.0.hardmasked.dict
# GTF/GFF file for V3
# gtf_file = /shares/tmockler_share/clizarraga/bdaccessions/Annotations/Bdist_V3/Brachypodium_distachyon.mainGenome.all.gtf
gtf_file = /shares/tmockler_share/clizarraga/Brachypodium_distachyon/Phytozome/v3.1/annotation/Bdistachyon_314_v3.1.gene_exons.gtf
# gff_file = /shares/tmockler_share/clizarraga/bdaccessions/Annotations/Bdist_V3/Brachypodium_distachyon.mainGenome.all.gff3
gff_file = /shares/tmockler_share/clizarraga/Brachypodium_distachyon/Phytozome/v3.1/annotation/Bdistachyon_314_v3.1.gene_exons.gff3
# Scripts/Programs used to filter fastq files.
deinterleave = /home/clizarraga/Projects/PyPipeline/Tools/deinterleave_fastq.py
trimmomatic = /nfs4shares/bioinfosw/installs_current/Trimmomatic-0.32/trimmomatic-0.32.jar
# Variant Effect Predictor Options
# vep = /home/clizarraga/usr/local/ensembl-tools-release-78/scripts/variant_effect_predictor/variant_effect_predictor.pl
# vepcache = /home/clizarraga/usr/local/ensembl-tools-release-78/scripts/variant_effect_predictor/gtf2vep.pl
vep = /home/clizarraga/usr/local/ensembl-tools-release-82/scripts/variant_effect_predictor/variant_effect_predictor.pl
vepcache = /home/clizarraga/usr/local/ensembl-tools-release-82/scripts/variant_effect_predictor/gtf2vep.pl
# It's now the same as the normal gtf or gff file.
# vepgtf = /shares/tmockler_share/clizarraga/bdaccessions/Annotations/Bdist_V3/Brachypodium_distachyon.mainGenome.all.vep.gtf
# Python to use
python = /home/clizarraga/usr/virtualenvs/Py2VE/bin/python
[DIRECTORIES]
data_dir = /shares/tmockler_share/Data/Illumina/Brachypodium/downloads1.jgi-psf.org/downloads/Jvogel/fastq_120130/
reseq = /shares/tmockler_share/Data/Illumina/Brachypodium/Resequencing
filtered_dir = /home/clizarraga/bdaccessions/Data_Final
output_dir = /home/clizarraga/bdaccessions/Results
temp_dir = /home/clizarraga/bdaccessions/Temp
reads = /home/clizarraga/bdaccessions/Reads
combined = /home/clizarraga/bdaccessions/Combined
[FILENAMES]
# Input VCF to VEP filename
vepvcf = .raw.snps.vcf
vepoutvcf = .vep.snps.
[COMBINE_ACCESSIONS]
#### Accession = Prefix for combinable accessions
# 14 = BdTR11I
# 18 = BdTR8i
# 19 = Bis-1
# 20 = Kah-1
# 22 = Tek-4
11 = Bd21-3
[SINGLE_ACCESSIONS]
#### Accession = Prefix for single, quality control accessions
# 24 = Adi-12
# 25 = Adi-2
# # 26 = Bd18-1
# 27 = Bd2-3
# # 28 = BdTR10C
# 29 = BdTR11A
# 30 = BDTR11G
# 31 = BdTR13a
# 32 = BdTR13C
# 33 = BdTR1i
# 34 = BdTR2G
# 35 = BdTR5I
# 37 = BdTR9K
39 = Bd3-1
40 = Bd1-1
41 = Bd30-1
42 = BdTR12c
43 = Koz-3
[DATA]
### Number = Full Filename(s) Accession.<unknown>.<unknown>.fastq.gz
# 11 = Bd21-3.671.3.916.fastq.gz,Bd21-3.671.4.916.fastq.gz,Bd21-3.671.5.916.fastq.gz,Bd21-3.671.6.916.fastq.gz
# 14 = BdTR11I.1774.3.1601.fastq.gz,BdTR11I.1999.5.1704.fastq.gz
# 18 = BdTR8i.1883.4.1652.fastq.gz,BdTR8i.1957.4.1684.fastq.gz,BdTR8i.2038.4.1726.fastq.gz
# 19 = Bis-1.1883.7.1652.fastq.gz,Bis-1.1957.7.1684.fastq.gz,Bis-1.2038.2.1726.fastq.gz
# 20 = Kah-1.1885.7.1658.fastq.gz,Kah-1.1957.5.1684.fastq.gz
# 22 = Tek-4.1883.5.1652.fastq.gz,Tek-4.1957.6.1684.fastq.gz
# 24 = Adi-12.1737.5.1585.fastq.gz
# 25 = Adi-2.2001.4.1706.fastq.gz
# 26 = Bd18-1.1883.6.1652.fastq.gz
# 27 = Bd2-3.1710.3.1556.fastq.gz
# 28 = BdTR10C.1702.1.1553.fastq.gz
# 29 = BdTR11A.1909.1.1665.fastq.gz
# 30 = BdTR11G.1999.3.1704.fastq.gz
# 31 = BdTR13a.2152.3.1802.fastq.gz
# 32 = BdTR13C.1710.6.1556.fastq.gz
# 33 = BdTR1i.2152.1.1796.fastq.gz
# 34 = BdTR2G.1710.1.1556.fastq.gz
# 35 = BdTR5I.1710.5.1556.fastq.gz
# 37 = BdTR9K.1710.7.1556.fastq.gz
[NUMBER_MULTIPLE]
#### Number = Number of files per accession
11 = 4
# 14 = 2
# 18 = 3
# 19 = 3
# 20 = 2
# 22 = 2
# 24 = 1
# 25 = 1
# # 26 = 1
# 27 = 1
# # 28 = 1
# 29 = 1
# 30 = 1
# 31 = 1
# 32 = 1
# 33 = 1
# 34 = 1
# 35 = 1
# 37 = 1
39 = 1
40 = 1
41 = 1
42 = 1
43 = 1