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Commit 0f8de69b authored by Celine Noirot's avatar Celine Noirot
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Correct option for merging SNP

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workflows/rnaseqdenovo/components/gatkfilter.py
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...@@ -83,7 +83,8 @@ class GatkVariantFilter (Component): ...@@ -83,7 +83,8 @@ class GatkVariantFilter (Component):
# Merge SNP and indels # Merge SNP and indels
self.add_shell_execution(self.get_exec_path("java") + " " + xmx_option + " -jar " + self.get_exec_path("gatk") + " -T CombineVariants "\ self.add_shell_execution(self.get_exec_path("java") + " " + xmx_option + " -jar " + self.get_exec_path("gatk") + " -T CombineVariants "\
"--assumeIdenticalSamples --genotypemergeoption UNIQUIFY -R $1 --variant $2 --variant $3 -o $4 2>> $5", cmd_format='{EXE} {IN} {OUT}' , "--assumeIdenticalSamples -R $1 --variant:snp $2 --variant:indel $3 -o $4 \
-genotypeMergeOptions PRIORITIZE -priority snp,indel 2>> $5", cmd_format='{EXE} {IN} {OUT}' ,
inputs=[self.reference, self.snp_tagged, self.indel_tagged], outputs=[self.tmp_file, self.tmp_file_stderr] ) inputs=[self.reference, self.snp_tagged, self.indel_tagged], outputs=[self.tmp_file, self.tmp_file_stderr] )
# Discard no passing filters # Discard no passing filters
self.add_shell_execution(self.get_exec_path("java") + " " + xmx_option + " -jar " + self.get_exec_path("gatk") + " -T SelectVariants "\ self.add_shell_execution(self.get_exec_path("java") + " " + xmx_option + " -jar " + self.get_exec_path("gatk") + " -T SelectVariants "\
......
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