At a glance

Variants

33,178

SNVs

27,316

Indels

5,892

Ti/Tv

2.13

The number of SNVs and indels are computed independently, and their sum could be different from the number of records due to the presence of multiallelic variants.

Statistics

filename MNVs SNVs indels multiallelic SNV sites multiallelic sites no-ALTs others records samples
variants.stats 0 27316 5892 8 369 0 0 33178 1
filename ts tv ts/tv ts (1st ALT) tv (1st ALT) ts/tv (1st ALT)
variants.stats 18599 8725 2.13 18594 8717 2.13

ClinVar variant annotations

This report was generated without annotations. To see them, re-run the workflow without --skip_annotation.

Substitution types

Base substitutions aggregated across all samples (symmetrised by pairing).

Indels length

Insertion and deletion lengths aggregated across all samples.

Software versions

Name Version
Clair3 v1.0.8

Workflow parameters

Key Value
out_dir /home/usuario/epi2melabs/instances/wf-hereditary-cancer_01M2GGC8ZRPEP156W9D3WKNMV7/output
sv True
snp True
str False
mod True
bam_min_coverage 10
depth_window_size 25000
annotation False
phased True
include_all_ctgs False
output_report True
haplocheck False
igv True
cluster_merge_pos 150
min_sv_length 30
sv_benchmark False
ref_pct_full 0.1
var_pct_full 0.7
snp_min_af 0.08
indel_min_af 0.15
min_cov 2
min_mq 5
min_qual 2
min_contig_size 0
refine_snp_with_sv True
force_strand False
depth_intervals False
GVCF False
base_err 0.001
gq_bin_size 5
downsample_coverage False
downsample_coverage_target 60
downsample_coverage_margin 1.1
output_xam_fmt bam
alignment_report_coverage_threshold 30
threads 4
ubam_map_threads 8
ubam_sort_threads 3
ubam_bam2fq_threads 1
modkit_threads 4
sample_name OMICS_14
bam /var/lib/minknow/data/20260902/HCP_sample_4_5_6/20260902_1532_P2S-03417-B_PBM52225_4f92217b/bam_pass/barcode05
store_dir /home/usuario/epi2melabs/data
sv_benchmark_vcf None
sv_benchmark_bed None
coverage_bed /home/usuario/epi2melabs/data/nanoporetech/wf-hereditary-cancer-coverage-bed/1/HCP_Exon.bed
ref /home/usuario/epi2melabs/data/nanoporetech/wf-hereditary-cancer-ref/1/HCP_hg38_alt.masked.fasta
bed /home/usuario/epi2melabs/data/nanoporetech/wf-hereditary-cancer-bed/1/HCP_Gene.bed
sex None
mitogenome None
override_basecaller_cfg None
clair3_model_path None
ctg_name None
vcf_fn None
tr_bed None
min_read_support auto
min_read_support_limit 2
sniffles_args None
modkit_args None
partner None