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Calls the bams pulled down from firehose cleaned by default 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5188 348d0f76-0448-11de-a6fe-93d51630548a
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corin 2011-02-03 18:34:07 +00:00
parent a22ea53665
commit ce2866122d
1 changed files with 10 additions and 0 deletions
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10
shell/getFirehosePipelineYaml.sh
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@ -114,3 +114,13 @@ END {
printf "\n ]" printf "\n ]"
print "\n}" print "\n}"
}' > $PIPELINE_YAML_FILE }' > $PIPELINE_YAML_FILE
hg19=`grep "assembly19" -c $PIPELINE_YAML_FILE`
if [ "$hg19" -ne 0 ]; then
sed 's/\/humgen.*rod/\/humgen\/gsa-hpprojects\/GATK\/data\/dbsnp_132_b37.vcf/' $PIPELINE_YAML_FILE > yaml2
mv yaml2 $PIPELINE_YAML_FILE
fi
sed 's/recalibrat/clean/' $PIPELINE_YAML_FILE > yaml2
mv yaml2 $PIPELINE_YAML_FILE