Commit 631cfa97 authored by Brandi Cantarel's avatar Brandi Cantarel

adding missing modules

parent 16480566
......@@ -152,7 +152,7 @@ process gatk {
file("final.gatkpanel.vcf.gz") into gatkvcf
script:
"""
module load gatk/3.5 bedtools/2.25.0 snpeff/4.2 vcftools/0.1.11
module load gatk/3.5 bedtools/2.25.0 python/2.7.x-anaconda snpeff/4.2 vcftools/0.1.11
java -Xmx16g -jar \$GATK_JAR -R ${gatkref} -D ${dbsnp} -T GenotypeGVCFs -o final.gatk.vcf -nt 4 --variant ${(gvcf as List).join(' --variant ')}
java -Xmx16g -jar \$GATK_JAR -R ${gatkref} -T VariantFiltration -V final.gatk.vcf -window 35 -cluster 3 -filterName FS -filter "FS > 30.0" -filterName QD -filter "QD < 2.0" -o final.filtgatk.vcf
vcf-annotate -n --fill-type final.filtgatk.vcf | java -jar \$SNPEFF_HOME/SnpSift.jar filter '((QUAL >= 10) & (MQ > 40) & (DP >= 10))' |bgzip > final.gatkpanel.vcf.gz
......@@ -171,7 +171,7 @@ process mpileup {
file("final.sampanel.vcf.gz") into samvcf
script:
"""
module load samtools/intel/1.3 bedtools/2.25.0 bcftools/intel/1.3 snpeff/4.2 vcftools/0.1.11
module load python/2.7.x-anaconda samtools/intel/1.3 bedtools/2.25.0 bcftools/intel/1.3 snpeff/4.2 vcftools/0.1.11
ls *.bam > final.bam.list
samtools mpileup -t 'AD,ADF,ADR,INFO/AD,SP' -ug -Q20 -C50 -f ${index_path}/genome.fa -b final.bam.list | bcftools call --format-fields gq,gp -vmO z -o final.sam.vcf.gz
vcf-annotate -n --fill-type final.sam.vcf.gz | java -jar \$SNPEFF_HOME/SnpSift.jar filter '((QUAL >= 10) & (MQ >= 20) & (DP >= 10))' |bgzip > final.sampanel.vcf.gz
......@@ -190,7 +190,7 @@ process speedseq {
file("final.complex.vcf.gz") into complexvcf
script:
"""
module load samtools/intel/1.3 bedtools/2.25.0 bcftools/intel/1.3 snpeff/4.2 speedseq/20160506 vcftools/0.1.11
module load python/2.7.x-anaconda samtools/intel/1.3 bedtools/2.25.0 bcftools/intel/1.3 snpeff/4.2 speedseq/20160506 vcftools/0.1.11
speedseq var -q 10 -t 32 -o final.ssvar ${index_path}/genome.fa ${gbam}
vcf-annotate -n --fill-type -n final.ssvar.vcf.gz | java -jar \$SNPEFF_HOME/SnpSift.jar filter '((QUAL >= 10) & (DP >= 10))' |bgzip > final.sspanel.vcf.gz
java -Xmx10g -jar \$SNPEFF_HOME/SnpSift.jar filter "(TYPE='complex')" final.sspanel.vcf.gz |bgzip> final.complex.vcf.gz
......@@ -210,7 +210,7 @@ process integrate {
file("final.integrate.vcf.gz") into finalvcf
script:
"""
module load bedtools/2.25.0 snpeff/4.2 bcftools/intel/1.3 samtools/intel/1.3 jags/4.2.0
module load python/2.7.x-anaconda bedtools/2.25.0 snpeff/4.2 bcftools/intel/1.3 samtools/intel/1.3 jags/4.2.0
module load vcftools/0.1.11
zcat ${ssvcf} | bedtools intersect -v -header -a stdin -b ${complex} | bgzip > ss.shuff.vcf.gz
vcf-shuffle-cols -t ${ssvcf} ${gvcf} | vcf-sort | bedtools intersect -v -header -a stdin -b ${complex} | bgzip > gatk.shuff.vcf.gz
......
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