Version 6.0.0

[henrikstranneheim]

Update Programs

• VEP => 90.X (script dir: 91; cache 91.X)
• GATK => 3.7 to 3.8
• TIDDIT => 1.1.6 to 2.0.3
• Bcftools => 1.4.1 to 1.6
• Samtools => 1.4.1 to 1.6
• Htslib => 1.4.1 to 1.6
• Picardtools => 2.9.1 => 2.14.1
• Peddy => 0.3.1
• Multiqc => 1.4

New Programs

• Rtg-tools
• Bcftools mpileup

Update References

• Clinvar 20170501 => 20171029
• Swegen_SV 20170830

New Annotations

• GnomAD (AF, AF_POPMAX)
• Clinvar (CLNVID)
• Swegen (swegenAF)
• MaxEntScan (VEP)

Removed Annotations

• Exac

New Programs

• Frequency_filter
• Vcf2cytosure

Removed Programs

• Madeline
• Bwa aln
• Bwa sempe
• GATK phasebytransmission
• GATK readbackphasing
• Annovar
• Samtools mpileup
• Removeredundant

New Flags

• program_source_environment_command
• module_source_environment_command
• pfrequency_filter
• psamtools_subsample_mt
• vcf2cytosure_exclude_filter
• vcf2cytosure_freq
• vcf2cytosure_freq_tag
• vf2cytosure_no_filter
• vcf2cytosure_var_size
• vep_plugins_dir_paths

Update Flags

• source_environment_commands -> source_main_environment_commands

Flags made boolean

• dry_run_all
• java_use_large_pages
• reduce_io
• replace_iupac
• bash_set_errexit
• bash_set_nounset
• bash_set_pipefail
• bwa_mem_hla
• bwa_mem_cram
• sambamba_depth_noduplicates
• sv_vt_decompose
• sv_bcftools_view_filter
• sv_svdb_query
• sv_vcfanno
• sv_genmod_filter
• sv_combinevariantcallsets_bcf_file
• sv_vcfparser_vep_transcripts
• sv_rankvariant_binary_file
• sv_vcfparser_per_gene
• sv_genmod_annotate_regions
• gatk_disable_auto_index_and_file_lock
• gatk_baserecalibration_disable_indel_qual
• gatk_haplotypecaller_no_soft_clipped_bases
• gatk_genotypegvcfs_all_sites
• gatk_concatenate_genotypegvcfs_bcf_file
• gatk_variantrecalibration_dp_annotation
• gatk_variantrecalibration_snv_max_gaussians
• gatk_variantrecalibration_indel_max_gaussians
• gatk_combinevariantcallsets_bcf_file
• vt_decompose
• vt_normalize
• vt_uniq
• vt_missing_alt_allele
• frequency_genmod_filter
• vcfparser_vep_transcripts
• snpeff_ann
• genmod_annotate_regions
• rankvariant_binary_file
• markduplicates_picardtools_markduplicates
• markduplicates_sambamba_markdup

MIP Changes

• Split of mip_install.pl into perl_install.pl (perl & cpanm req perl v.5.10) and mip_install.pl (req perl v.5.18)
• Removed use of perl_install and instead use perlbrew with cpanm
• Now support perl version 5.26.0
• Added cpanfile for installing cpanm deps
• Added log to mip_install
• Removed associated_programs from analysis_config
• Automatically update sv_prioritization flag depending on analysis_type
• Added option to qccollect to use path as well as outdirectory and outfile in qc_sample_info
• Removed evaluation of wes and PCT_TARGET_BASES_30X in qccollect
• Added metafile_tag to qc_sample_info
• Added get and set sub for recording and extracting info in qc_sample_info
• Allow sourcing of different environments for each module in addition to main env
• Add option flag to source specific programs environments using program_source_environment_command
• Removed bcftools filtering from bcftools mpileup
• Needed to split this from Vt recipe as rhocall and genmod uses different versions of python within the same shell
• Clnvar has removed the CLNACC and replaced it with a variant id in the vcf ID column. When MIP downloads clinvar it will preprocess the clinvar vcf as follows:
  1. Relay the clinvar variant id from the clinvar vcf ID column as a vcf info key in the same file.
  2. Add a new vcf INFO key pair and header as; '##INFO=<ID=CLNVID,Number=1,Type=Integer,Description="ClinVar Variation ID">'
• Added eval of peddy stderr info to analysisrunstatus
• Added sub sampling of MT BAM for viewing in Scout
• Added vcf2cytosure
• Added embryo for wts and cancer pipeline
• Major refactoring of mip.pl and mip_install.pl
• Added tests and test procedure