At a glance

Sites (of which variants)

60 (60)

SNVs

52

Indels

8

Ti/Tv

2.47

Statistics

filename MNVs SNVs indels multiallelic SNV sites multiallelic sites no-ALTs others records samples
vcfstats.txt 0 52 8 0 0 0 0 60 1
filename ts tv ts/tv ts (1st ALT) tv (1st ALT) ts/tv (1st ALT)
vcfstats.txt 37 15 2.47 37 15 2.47

Variant allele frequencies

Variant allele frequency (VAF) comparison between normal (x-axis) and tumor (y-axis). The tooltips display the tumor VAF of each site.

N sites No ALTS PASS not PASS Type VAF > 0.20 VAF > 0.10 VAF > 0.05
60 0 42 18 Tumor 51 55 60
Normal 7 7 7

Mutational characterisation

This section shows the type of changes found and their distribution.

Change distribution
96 mutational profile

ClinVar variant annotations

The SnpEff annotation tool has been used to annotate with ClinVar. If any variants have ClinVar annotations, they will appear in a table below. Please note, this table excludes variants with 'Benign' or 'Likely benign' significance, however these variants will appear in the VCF output by the workflow. For further details on the terms in the 'Significance' column, please visit this page.

No ClinVar sites to report.

Software versions

Name Version
run_clairs 0.1.5
bcftools 1.16

Workflow parameters

Key Value
sv True
mod True
snv True
bam_normal wf-somatic-variation-demo/demo_normal.bam
bam_tumor wf-somatic-variation-demo/demo_tumor.bam
sample_name SAMPLE
ref wf-somatic-variation-demo/GCA_000001405.15_GRCh38_no_alt_analysis_set_chr20.fna
bed None
tr_bed None
annotation True
out_dir wf-somatic-variation
ubam_map_threads 2
ubam_sort_threads 1
ubam_bam2fq_threads 1
annotation_threads 4
tumor_min_coverage 0
normal_min_coverage 0
depth_window_size 50000
depth_intervals False
basecaller_cfg dna_r10.4.1_e8.2_400bps_sup@v3.5.2
normal_vcf None
hybrid_mode_vcf None
genotyping_mode_vcf None
skip_haplotype_filter False
haplotype_filter_threads 4
ctg_name EMPTY
include_all_ctgs False
snv_min_af 0.05
indel_min_af 0.05
min_contig_size 0
min_qual 8
min_cov 4
use_longphase True
use_longphase_intermediate True
print_ref_calls False
print_germline_calls False
germline True
phase_normal False
clairs_debug False
fast_mode False
clair3_phase_vcf False
clair3_ref_pct_full 0.1
clair3_var_pct_full 0.7
clair3_min_mq 5
GVCF False
vcf_fn EMPTY
min_sv_length 20
nanomonsv_get_threads 4
classify_insert False
qv None
force_strand False
modkit_args None
dss_threads 1
modkit_threads 4
help False
version False
aws_image_prefix None
aws_queue None
disable_ping False
monochrome_logs False
validate_params True
show_hidden_params False
schema_ignore_params show_hidden_params,validate_params,monochrome_logs,aws_queue,aws_image_prefix,wf
wf {'example_cmd': ['--snv', '--sv', '--mod', '--sample_name MYSAMPLE', '--ref wf-somatic-variation-demo/GCA_000001405.15_GRCh38_no_alt_analysis_set_chr20.fna', '--bed wf-somatic-variation-demo/demo.bed', '--bam_normal wf-somatic-variation-demo/demo_normal.bam', '--bam_tumor wf-somatic-variation-demo/demo_tumor.bam', '--basecaller_cfg dna_r10.4.1_e8.2_400bps_sup@v3.5.2', '--normal_min_coverage 0', '--tumor_min_coverage 0'], 'container_sha': 'sha534c3242546d2cf9d8d56a2dd3e35643ac736919', 'container_snp_sha': 'shae351df8d88fcab571a346a1cff7b48237536bd0f', 'container_sv_sha': 'shaa94980c361625f0d50dcaf5bcf2abd005d57ec2c', 'container_mod_sha': 'shac81dbea5f824cc43fd7aeb9ad99b4efe1503216e', 'common_sha': 'sha0a6dc21fac17291f4acb2e0f67bcdec7bf63e6b7', 'snpeff_tag': 'sha4f289afaf754c7a3e0b9ffb6c0b5be0f89a5cf04', 'dss_sha': 'sha75990241a7936bcb0dc9a72f2bd9623b40a02e4e', 'agent': 'cw-ci'}