From e5a54f526ec841568ad45c3ef0dde7f4ec8b2f9a Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Tue, 11 Aug 2020 20:14:48 -0500
Subject: [PATCH] update small docker/dnanexus incompatobility
---
variants/germline_vc.sh | 4 +++-
variants/somatic_vc.sh | 1 +
2 files changed, 4 insertions(+), 1 deletion(-)
diff --git a/variants/germline_vc.sh b/variants/germline_vc.sh
index ac2c1d7..c81b05f 100755
--- a/variants/germline_vc.sh
+++ b/variants/germline_vc.sh
@@ -86,7 +86,9 @@ then
for i in *.bam; do
bamlist="$bamlist --bam ${PWD}/${i}"
done
- cut -f 1 $fbsplit | parallel --memfree 2G --delay 1 --jobs 0 "freebayes -f ${index_path}/genome.fa --min-mapping-quality 0 --min-base-quality 20 --min-coverage 10 --min-alternate-fraction 0.01 -C 3 --use-best-n-alleles 3 -r {} ${bamlist} > fb.{}.vcf"
+ #--memfree 2G for DNANexus
+
+ cut -f 1 $fbsplit | parallel --delay 1 --jobs 0 "freebayes -f ${index_path}/genome.fa --min-mapping-quality 0 --min-base-quality 20 --min-coverage 10 --min-alternate-fraction 0.01 -C 3 --use-best-n-alleles 3 -r {} ${bamlist} > fb.{}.vcf"
vcf-concat fb.*.vcf | vcf-sort | vcf-annotate -n --fill-type | bcftools norm -c s -f ${reffa} -w 10 -O z -o ${pair_id}.fb.vcf.gz -
elif [[ $algo == 'platypus' ]]
then
diff --git a/variants/somatic_vc.sh b/variants/somatic_vc.sh
index d3701aa..f3461f0 100755
--- a/variants/somatic_vc.sh
+++ b/variants/somatic_vc.sh
@@ -142,6 +142,7 @@ then
elif [ $algo == 'shimmer' ]
then
module load R/3.6.1-gccmkl
+ module rm perl/5.18.2
shimmer.pl --minqual 25 --ref ${reffa} ${normal} ${tumor} --outdir shimmer 2> shimmer.err
perl $baseDir/add_readct_shimmer.pl
module rm java/oracle/jdk1.7.0_51
--
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