Do not gzip fastqs for bowtie
Correctly handle pre-aligned inputs when GATK not installed. Thanks to Stephan Pabinger
Fix samtools output to be compatible with tools that cannot handle VCFv4.2
Improve documentation of indelcaller argument. Thanks to @lbeltrame
Provide flag to skip external version checks when running bcbio inside docker containers
Provide external function to load a sample configuration file. Enables loading of reference data from within a docker context
Avoid issue with pandas and google-api-python-client: pydata/pandas#8581 Thanks to Jonathan Epstein
Move files to sample specific directory during assembly.

This avoids race conditions that can happen when moving the files back.
For joint called samples ensure we pass along each individual sample for downstream processing but still skip splitting into individual VCFs
cnvkit: add to automated installation and finish implementation of cancer and population calling (which uses single sample with uniform background). Update unit tests to include segmented regions for analysis
Enable CombineGVCFs to use maximum memory for associated cores to handle merging of large sample groups. Thanks to @lpantano
Use one consequence only with VEP if clinical_reporting is active

When looking for variants at the gene / exon level, sometimes it is
desirable to have only one consequence annotated, in particular for data
in clinical research. bcbio-nextgen already does this with snpEff
(-canonical option), but so far it was not used by VEP.

This patch adds this behavior (defaulting to false, hence not breaking
existing setups. It does so by using VEP's --pick option, introduced in
version 75.

From the VEP docs:

"Pick once line of consequence data per variant, including
transcript-specific columns. Consequences are chosen by the canonical,
biotype status and length of the transcript, along with the ranking of
the consequence type according to this table. This is the best method to
use if you are interested only in one consequence per variant. "
Ensure somatic options applied to single tumor, no normal calling with FreeBayes. Thanks to @mjafin
Merge pull request #648 from lbeltrame/vep-single-effect-clinical-reporting

Use one consequence only with VEP if clinical_reporting is active
add scripts to utils to merge FASTQ and BAM files
add bamtools in case other tool fail and get script in utils
add docs

Update configuration.rst

fix typos

Update configuration.rst

fix command format

Update configuration.rst

getting correct command format
Merge pull request #649 from lpantano/upstream

add script to merge FASTQ and BAM files
Initial integration work on THetA for calculating tumor heterogeneity and normal contamination. Thanks to @etal
Merge pull request #637 from saketkc/bowtie_fix

Do not gzip fastqs for bowtie