Bump canFam3 resource to use new dbSNP
Documentation: update todo list with latest work. Add suggestion for recent gcc to intall docs (chapmanb/homebrew-cbl#9). Improve VM instructions for MacOSX, thanks to Glen Otero
Support CRAM files as input to pipeline, including retrieval of sub-regions based on variant_region input. Uses new CRAM region support in biobambam (gt1/biobambam#36)
Baseline support for SNAP aligner for testing purposes. Does not yet include automatic index creation as part of integration.
Ensure memory specification modifier is uppercase to be compatible with sambamba. Tries to introduce forward compatibility for any swaps from samtools to sambamba. Fixes #425
Ensure input CRAM files have indexes, splitting indexing from compression and using scramble C indexing implementation
Fixes for FreeBayes filtering AF extraction and sample selection test to support latest bcftools release candidate
Remove namespace packaging of bcbio to avoid getting __init__.py removed by pip. Add prettyplotlib for variant plots
Structural variation improvements. cn.mops: do not split regional analyses by chromsome. delly: correctly avoid running on chromosomes with variant regions, handle remapping sample names. lumpy: remove Approach filter which is too stringent
Increase version for canFam3 to point to new dbSNP file. #386
Avoid too long commandlines by writing regions to intermediate file before passing to samtools commandline #386
Add unique naming for FreeBayes and GATK hard filters to avoid losing unique filters during merges. Thanks to Severine Catreux
Delly filters based on high quality variant pairs: performs sample based filtering using parameters tuned to NA12878 structural variant calling
Upload structural variant calls in final output directory using same approach and naming as SNP/indels
Use sambamba with support for regional retrieval using a BED file to avoid command line length issues. #386
Ensure retrieval of samples from cn.mops combined output when sample names are numeric and R adds an X prefit on output to BED
Add base support for latest Zebrafish genome build: Zv9
Document process for adding new organism support to bcbio-nextgen
Fix variant region selection parameter to be compatible with bcftools rc8. Expose provenance.do functionality for finding bash
Ensure non-overlapping read names on CRAM to fastq preparation using sequential part-based naming. Write steps as shell script and run in serial to avoid open file handle errors for large inputs.