7.1.10

• Added BAM contigs set to allow for single ladies to get a proper check sex (no pun intended:). Actually it is for all female only analyses.

7.1.9

• Fix possible race condition between expansionhunter and sambamba depth

7.1.8

• Limit mixed case to wes contigs

7.1.7

• Use MQ annotation when running GATK VariantRecalibration for SNV

7.1.6

• Added correct recipe name to qc_sample_info.yaml

7.1.5

• Increased sv_varianteffectpredictor memory parameter 9 -> 18 Gb

7.1.4

• Fixed bug with outfile path when mitochondria contig is not part of gene panel

v7.1.3

[7.1.3]

• Increased sv_varianteffectpredictor memory parameter 8 -> 9 Gb

v7.1.2

[7.1.2]

• Update samtools_subsample_mt to fix bug in downsampling of MT bam
• Fixed bug when skipping evaluation in QC_collect

v7.1.0

[7.1.0]

• Updated TIDDIT to enable faster processing
• Updated GATK for faster haplotypecalling
• Removed plink memory allocation from rd_dna_vcf_rerun
• Increased memory allocation for vep (snv/indel)
• Allow "unknown" sex when using expansionhunter by then not using gender in expansionhunter CLI
• Updated stranger to version 0.5.4 to avoid repeat id warnings
• Increased recipe memory for plink and vcf2cytosure
• Added removal of genomicsDB dir from potential previous analysis as it causes gatk genotyping to crash

Tools

• TIDDIT: 2.5.0 -> 2.7.1
• bcftools: 1.9-h4da6232_0 -> 1.9=ha228f0b_4
• bioconductor-deseq2: 1.18.1=r3.4.1_1 -> 1.22.1=r351hf484d3e_0
• bioconductor-tximport: 1.8.0=r341_0 -> 1.12.0=r351_0
• GATK: 4.1.0.0-0 -> 4.1.2.0-1
• samtools: 1.9-h8ee4bcc_1 -> 1.9=h8571acd_11
• stranger: 0.5.1 -> 0.5.4