10.0.0

• Remove unused recipe split_fastq_file
• Align with the same bwa mem options as used by Broad
  • Fixed number of bases in each batch
  • Use bwa mem instead of run-bwamem for alignment to grch38
• Use Chanjo repos Docker file instead of MIPs
• Removed support to run bcftools_mpileup as a variant caller
• Added perl and MIP docker file and use it in recipes
• Removed PATH check for proxy bins
• Switched to using container manager instead of proxy bins in recipes
• Removed support to run variant_integrity
• Added deepvariant as variant caller and glnexus to merge samples to case vcf

Tools

arriba: v1.2.0 -> v2.1.0
bedtools: 2.29.0 -> 2.30.0
bwa-mem2 2.0 -> 2.2
chanjo: 4.2.0 -> 4.6
chromograph: 1.0.1 -> 1.1
cyrius: v1.0 -> v1.1
deepvariant: 1.1.0
delly: 0.8.1 -> 0.8.7
gatk: v4.1.8.1 -> v4.2.0.0
glnexus: v1.3.1
megafusion: 66a3a80
multiqc: 1.9 -> 1.10.1
pdfmerger: v1.0
picardtools: 2.23.4 -> 2.25.0
preseq: 2.0.3 -> 3.1.2
rseqc: 3.0.1 -> 4.0.0
rtg-tools: 3.10.1 -> 3.12
salmon: 0.12.0 -> 1.4.0
smncopynumbercaller: 4b2c1ad -> v1.1.1
star: 2.7.4a -> 2.7.8a
stranger: 0.7 -> 0.7.1
svdb: 2.2.0 -> 2.4.0--py37h77a2a36_4
tiddit: 2.8.1 -> 2.12.1
upd: 0.1 -> 0.1.1

References

• clinvar_20200905 -> clinvar_20210415
• VEP cache: 100 -> 103.1
• grch37_gencode_v19_ctat_lib_plug-n-play_-apr032020-.tar.gz -> grch37_gencode_v19_CTAT_lib_Mar012021.plug-n-play.tar.gz
• grch38_gencode_v31_ctat_lib_plug-n-play_-apr062020-.tar.gz -> grch38_gencode_v37_CTAT_lib_Mar012021.plug-n-play.tar.gz
• gencode annotation: v34 -> v37