Closed syansanofi closed 3 years ago
Issue New gatk version requires small change to template for BaseRecalibrator tool and PrintReads becomes ApplyBQSR
Old
https://github.com/epam/fonda/blob/4a651caa0ab4bdb4ff92516d2294331c9723f134/src/main/resources/templates/amplicon_gatk_recalibrate_tool_template.txt#L2-L3
New [(${toolFields.java})] -Xmx10g -Djava.io.tmpdir=[(${tmpOutdir})] -jar [(${toolFields.gatk})] BaseRecalibrator -R [(${databaseFields.genome})] -I [(${additionalFields.bam})] --use-original-qualities true -knownSites [(${databaseFields.dbSnp})] -knownSites [(${databaseFields.knownIndelsMills})] -knownSites [(${databaseFields.knownIndelsPhase1})] -o [(${additionalFields.recalTable})]
[(${toolFields.java})] -Xmx10g -Djava.io.tmpdir=[(${tmpOutdir})] -jar [(${toolFields.gatk})] BaseRecalibrator -R [(${databaseFields.genome})] -I [(${additionalFields.bam})] --use-original-qualities true -knownSites [(${databaseFields.dbSnp})] -knownSites [(${databaseFields.knownIndelsMills})] -knownSites [(${databaseFields.knownIndelsPhase1})] -o [(${additionalFields.recalTable})]
[(${toolFields.java})] -Xmx10g -Djava.io.tmpdir=[(${tmpOutdir})] -jar [(${toolFields.gatk})] ApplyBQSR -R [(${databaseFields.genome})] -I [(${additionalFields.bam})] -bqsr [(${additionalFields.recalTable})] -o [(${additionalFields.recalBam})]
Diff BaseRecalibrator
--disable_indel_quals
--use-original-qualities true
PrintReads / ApplyBQSR
-BQSR
-bqsr
Issue New gatk version requires small change to template for BaseRecalibrator tool and PrintReads becomes ApplyBQSR
Old
https://github.com/epam/fonda/blob/4a651caa0ab4bdb4ff92516d2294331c9723f134/src/main/resources/templates/amplicon_gatk_recalibrate_tool_template.txt#L2-L3
New
[(${toolFields.java})] -Xmx10g -Djava.io.tmpdir=[(${tmpOutdir})] -jar [(${toolFields.gatk})] BaseRecalibrator -R [(${databaseFields.genome})] -I [(${additionalFields.bam})] --use-original-qualities true -knownSites [(${databaseFields.dbSnp})] -knownSites [(${databaseFields.knownIndelsMills})] -knownSites [(${databaseFields.knownIndelsPhase1})] -o [(${additionalFields.recalTable})]
[(${toolFields.java})] -Xmx10g -Djava.io.tmpdir=[(${tmpOutdir})] -jar [(${toolFields.gatk})] ApplyBQSR -R [(${databaseFields.genome})] -I [(${additionalFields.bam})] -bqsr [(${additionalFields.recalTable})] -o [(${additionalFields.recalBam})]
Diff BaseRecalibrator
--disable_indel_quals
--use-original-qualities true
PrintReads / ApplyBQSR
-BQSR
becomes-bqsr