Tolerate non-bcftools indexes

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ProcessVariantsHandler.java

@@ -485,7 +485,16 @@ public static String getVCFLineCount(File vcf, Logger log, boolean passOnly, boo
                 throw new PipelineJobException("bcftools VCF count cannot be used with passOnly");
             }
 
-            return countUsingBcfTools(vcf, log);
+            try
+            {
+                return countUsingBcfTools(vcf, log);
+            }
+            catch (PipelineJobException e)
+            {
+                // ignore and continue:
+                log.error("Cannot count variants using bcftools, this index might have been created using another tool");
+            }
+
         }
 
         String cat = vcf.getName().endsWith(".gz") ? "zcat" : "cat";