Update amplicon_gatk_recalibrate_tool_template

[syansanofi]

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

• Remove --disable_indel_quals
• Add --use-original-qualities true

PrintReads / ApplyBQSR

• -BQSR becomes -bqsr