--- a/tb_profiler_profile.xml	Fri Aug 16 16:26:31 2019 -0400
+++ b/tb_profiler_profile.xml	Tue Oct 15 14:35:47 2019 -0400
@@ -41,6 +41,7 @@
 
             --threads "\${GALAXY_SLOTS:-1}"
         #if $advanced.options == 'yes'
+            '${advanced.call_whole_genome}'
             --call_method '${advanced.call_method}'
             --min_gene_frac '${advanced.min_gene_frac}'
             --mapper '${advanced.mapper}'
@@ -58,7 +59,7 @@
         #if str($fastq_or_bam.input_select) != "bam"
             && mv bam/tbprofiler.bam '${output_bam}'
         #end if
-        && bcftools view -Ov -o'${output_vcf}' vcf/tbprofiler.targets.csq.bcf
+        && bcftools view -Ov -o'${output_vcf}' vcf/tbprofiler.targets.csq.vcf.gz
         #if $output_format == "pdf"
             && mv results/tbprofiler.results.pdf '${output_pdf}'
         #else if $output_format == "txt"
@@ -109,6 +110,8 @@
                     <option value="high">High</option>
                     <option value="optimise">Optimise</option>
                 </param>
+                <param label="Call variants on the whole genome" type="boolean" argument="--call_whole_genome" 
+                    truevalue="--call_whole_genome" falsevalue="" help="Call variants on whole genome (Useful if you need to use whole genome variants later)" />
                 <param label="Minimum coverage fraction to infer deletion" type="float" help="Used to infer a deletion if the fraction of a gene covered falls below this value." argument="--min_gene_frac" value="0.9" />
 
                 <param name="min_depth" label="Min Depth" type="integer" value="10" help="Minimum depth required to call variant. Bases with depth below this cutoff will be marked as missing (default: 10)"/>
@@ -173,7 +176,7 @@
 Summary
 =======
 
-The pipeline aligns reads to the H37Rv reference using bowtie2, BWA or minimap2 and then calls variants using SAMtools. These variants are then compared to a drug-resistance database. We also predict the number of reads supporting drug resistance variants as an insight into hetero-resistance (not applicable for minION data).
+The pipeline aligns reads to the H37Rv reference using bowtie2, BWA or minimap2 and then calls variants using GATK. These variants are then compared to a drug-resistance database. We also predict the number of reads supporting drug resistance variants as an insight into hetero-resistance (not applicable for minION data).
 
 Produces a JSON output file by default.