inputs

README.md

@@ -64,14 +64,23 @@ FreeBayes is very slow with single thread, using the scripts/freebayes-parallele
 
 ```bash
 freebayes-parallel <(fasta_generate_regions.py ref.fa.fai 100000) 36 \
-    --genotype-qualities -f ref.fa aln.bam >var.vcf
+    --genotype-qualities --max-complex-gap 75 -f ref.fa aln.bam >var.vcf
 ```
 
+##### Per sample running time
 
+Settings:
+
+Disk size: 400
+
+Cluster: OnDemand ecs.sn1ne.8xlarge img-ubuntu-vpc
+
+sample: 30x WGS
+
+**3h**
 
 ####**Reference**
 
 1. Freebayes GitHub <https://github.com/ekg/freebayes>
 2. Freebayes paper <https://arxiv.org/abs/1207.3907>
-
 3. Freebayes parallel problem fix <https://github.com/ekg/freebayes/issues/301>

tasks/Freebayes.wdl

@@ -15,7 +15,7 @@ task Freebayes {
 		set -o pipefail
 		set -e	
 		nt=$(nproc)
-		/opt/freebayes/scripts/freebayes-parallel <(/opt/freebayes/scripts/fasta_generate_regions.py ${ref_dir}/${ref_fa_fai} 100000) $nt -f ${ref_dir}/${fasta} --genotype-qualities ${Dedup_bam} > ${sample}_fb.vcf
+		/opt/freebayes/scripts/freebayes-parallel <(/opt/freebayes/scripts/fasta_generate_regions.py ${ref_dir}/${ref_fa_fai} 100000) $nt -f ${ref_dir}/${fasta} --genotype-qualities --max-complex-gap 75 ${Dedup_bam} > ${sample}_fb.vcf
 	>>>
 
 	runtime {