Twist_Solid v0.9.0

Release notes v0.9.0

UMI

Possibility to analyse the data using UMIs. UMI analysis for all or selected samples can be achive by adding an extra column in samples.tsv named deduplication. In this column all samples marked with umi will be run using UMIs. Some results will be additionally be created without using UMIs (bam, vcf, MSI, TMB, MultiQC).
UMI read consensus and filtering are performed by Fgbio.

Reference creation pipeline

Use the coming release v0.10.0 for this.

Changes in output files

Added UMI output files
Modified files as adotion to reworked annotation modules
New reference output files need update, please use next version (v0.10.0)

Changes in config

Added config file for GRCh38
Reworked config_references.yaml
Reworked config_references_hg38.yaml

Added in hg19 config (VEP and UMI-changes):

vep:
 mode: --offline --cache --refseq

bwa_mem_realign_consensus_reads:
 container: "docker://hydragenetics/fgbio:2.1.0"

fgbio_call_and_filter_consensus_reads:
 container: "docker://hydragenetics/fgbio:2.1.0"
 max_base_error_rate: "0.2"
 min_reads_call: "1 0 0"
 min_reads_filter: "1 0 0"
 min_input_base_quality_call: 20
 min_input_base_quality_filter: 30

fgbio_copy_umi_from_read_name:
 container: "docker://hydragenetics/fgbio:2.1.0"

fgbio_group_reads_by_umi:
 container: "docker://hydragenetics/fgbio:2.1.0"
 umi_strategy: paired

filter_vcf:
 snv_hard_filter_umi: "config/config_hard_filter_umi.yaml"
 snv_soft_filter_umi: "config/config_soft_filter_umi.yaml"

multiqc:
 container: "docker://hydragenetics/multiqc:1.11"
 reports:
  DNA:
   deduplication: ["mark_duplicates"]
  DNA_umi:
   config: "config/multiqc_config_dna.yaml"
   included_unit_types: ["N", "T"]
   deduplication: ["umi"]
   qc_files:
     - "qc/fastqc/{sample}{type}{flowcell}{lane}{barcode}fastq1_fastqc.zip"
     - "qc/fastqc/{sample}{type}{flowcell}{lane}{barcode}fastq2_fastqc.zip"
     - "qc/picard_collect_alignment_summary_metrics/{sample}{type}.alignment_summary_metrics.txt"
     - "qc/picard_collect_duplication_metrics/{sample}{type}.duplication_metrics.txt"
     - "qc/picard_collect_hs_metrics/{sample}{type}.HsMetrics.txt"
     - "qc/picard_collect_insert_size_metrics/{sample}{type}.insert_size_metrics.txt"
     - "qc/samtools_stats/{sample}{type}.samtools-stats.txt"
     - "qc/gatk_calculate_contamination/{sample}{type}.contamination.table"
     - "alignment/fgbio_group_reads_by_umi/{sample}_{type}.umi.histo.tsv"

samtools_merge_bam_umi:
 extra: "-c -p"

tmb_umi:
 af_lower_limit: 0.000
 af_upper_limit: 0.994
 af_germline_lower_limit: 0.3
 af_germline_upper_limit: 0.7
 artifacts: ""
 background_panel: ""
 db1000g_limit: 0.0001
 dp_limit: 300
 filter_genes: "/projects/wp1/nobackup/ngs/utveckling/Twist_DNA_DATA/tmb_filter_genes.txt"
 gnomad_limit: 0.0001
 vd_limit: 0
 nr_avg_germline_snvs: 0.0
 nssnv_tmb_correction: 0.84

vardict:
 allele_frequency_threshold_umi: "0.001"

Changes in resources (UMI + reference creation)

New reference resource file

Added UMI to ordinary resources file:
bwa_mem_realign_consensus_reads:
 mem_mb: 61440
 mem_per_cpu: 6144
 threads: 10
 time: "8:00:00"

fgbio_call_and_filter_consensus_reads:
 threads: 3
 mem_mb: 18432
 mem_per_cpu: 6144
 time: "8:00:00"

fgbio_group_reads_by_umi:
 time: "8:00:00"

Hydra modules with releases

• prealignment: v1.0.0 (No change)
• alignment: v0.5.0 (Adding support for UMIs using Fgbio)
• snv_indels: v0.3.0 (No change)
• annotation: v1.0.1 (Annotation order not fixed in module. Update pipeline to reflext this)
• filtering: v0.3.0 (Additional filtering features not affecting the pipeline)
• qc: v0.3.0 (No change)
• biomarker: v0.4.0 (No change)
• cnv_sv: v0.3.1 (No change)
• reports: v0.2.0 (No change)

Snakemake min version

7.18.0

Features

• 2 new TERT promoter variants (ee72af1)
• add umi support for cnvkit (979c816)
• add umi support for fuseq wes (a4d7139)
• add umi support for fuseq wes (522ac37)
• add umi support for gatkcnv (a2ce975)
• add umi support for hrd and msi (20560a2)
• add umi support for manta (8a703d9)
• add umi support for qc (89f673b)
• add umi support for tmb (9683d6b)
• added tmb gene filter. TMB uses hard filtered file for input (9e242a3)
• added umi choice to the pipeline (8e13b38)
• changes hard filtering to let more variants through (70606f3)
• hard filter for qci (9ae0a2f)
• min vaf configurable in vardict (303b5f7)
• rm need for ruleorder for copy rules using global wildcard constraints (ad15f6c)
• run msi w and wo umi (6766b18)
• umi in rna (6ccba4c)
• umi vcf filtering based on sample.tsv (4fdd999)
• update alignment module tag (ed33d45)
• update to v1.0.0 relaese of annotation (3fd0c7b)
• Update workflow/Snakefile with new alignment tag (e74398e)
• updated alignment module tag (62500dd)
• updated alignment module tag (341a3ba)
• updated module versions and adapted to these new versions (c4aa705)

Bug Fixes

• adapt to new umi alignment module (60a90b3)
• adopt to breaking change in vep rule (96b4b26)
• bugfix in get_vardict_min_af (cd503b7)
• bugfix in get_vardict_min_af (44d4b59)
• corrected gatk_mutect2 input files (442d62c)
• fix manta output files and rm unneaded umi rules in Snakefile (5ec7a33)
• fixed units.tsv and adaption of reference pipeline to new annotation module (9d0c926)
• gvcfs now have mosdepth umi coverage (cf3e9c6)
• manta to use original name, filtering wo <=, msi-sensor w correct output name (0a9960b)
• match output result from reference module (e2415d5)
• mosdepth should be run on entire bam file (8643bb2)
• msi (6578e7d)
• new common container compatible with filtering module v0.3.0 (28256f0)
• reinstate output vcf file (2b6607b)
• rm bai input for picard insert size metrics (4f8915f)
• rm umi on rna (086f8dc)
• umi fixes (9ce1a0b)
• update tag and only use umi for snv and indels (d6b1edc)
• updated alignment module tag (6207ed2)
• updated vcf filters (def213d)
• updated versions of snv_indels and annotation to fix compatilibilty issues (974dd27)
• use same hydra as in common container (v1.8.1) (d3f401e)