Pins for bcftools and freebayes

- Pin bcftools to 1.3.0 since 1.3.1 (samtools/bcftools#420) does not
  deal with Integer/Float issues from FreeBayes. GATK post-processing
  forces conversions to Integer for defined VCF attributes, causing
  failures. Prefer the 1.3.0 behavior of truncating to integers instead
  of failing.
- Update FreeBayes to latest version with fixes for gVCF and GQ.

contrib/flavor/ngs_pipeline_minimal/packages-conda.yaml

@@ -16,7 +16,7 @@ bio_nextgen:
   - bcbio-variation
   - bcbio-variation-recall
   - bcbreport
-  - bcftools
+  - bcftools=1.3.0
   - bedtools=2.24.0
   - biobambam
   - bowtie
@@ -35,7 +35,7 @@ bio_nextgen:
   - delly
   - express
   - fastqc
-  - freebayes=1.0.2
+  - freebayes=1.0.2.29
   - gatk
   - gatk-framework=3.5.21
   - geneimpacts