At a glance

Variants

153,218

SNVs

135,893

Indels

17,433

Ti/Tv

1.39

Statistics

filename MNVs SNVs indels multiallelic SNV sites multiallelic sites no-ALTs others records samples
variants.stats 0 135893 17433 72 1189 0 0 153218 1
filename ts tv ts/tv ts (1st ALT) tv (1st ALT) ts/tv (1st ALT)
variants.stats 78995 56970 1.39 78946 56918 1.39

ClinVar variant annotations

The SnpEff annotation tool has been used to annotate with ClinVar. Variants with ClinVar annotations will appear in the table below, ranked according to their significance. 'Pathogenic', 'Likely pathogenic', and 'Unknown significance' will be displayed first, in that order. Please note that variants classified as 'Benign' or 'Likely benign' are not reported in this table, but will appear in the VCF output by the workflow. For further details on the terms in the 'Significance' column, please visit this page.

Sample Chrom Pos Gene(s) ClinVar Significance Type Consequence HGVSc HGVSp
MY_SAMPLE chr20 36432094 DLGAP4 2362009 Uncertain significance SNV Missense variant NM_001365621.2:c.377G>A p.Arg126His
MY_SAMPLE chr20 57566161 PCK1 338910 Uncertain significance Microsatellite 3' UTR variant NM_002591.4:c.*390_*393delTGTG -
MY_SAMPLE chr20 58445684 VAPB 338953 Uncertain significance Microsatellite Non-coding transcript variant, 3' UTR variant NM_004738.5:c.*1485_*1486delGT -
MY_SAMPLE chr20 3234173 SLC4A11 262001 Conflicting interpretations of pathogenicity SNV Non-coding transcript variant, Synonymous variant NM_032034.4:c.481A>C p.Arg161Arg
MY_SAMPLE chr20 44429378 HNF4A 676884 Conflicting interpretations of pathogenicity SNV Intron variant NM_001030004.3:c.*4999T>C -
MY_SAMPLE chr20 7912993 HAO1 126884 Association SNV Intron variant NM_017545.3:c.545+1171T>C -
MY_SAMPLE chr20 7916402 HAO1 126885 Association SNV Intron variant NM_017545.3:c.290-1983G>A -
MY_SAMPLE chr20 7926296 HAO1 126887 Association SNV Intron variant NM_017545.3:c.289+8188C>T -
MY_SAMPLE chr20 7939957 HAO1 126890 Association SNV Intron variant NM_017545.3:c.137+329T>C -
MY_SAMPLE chr20 34269192 AHCY, ASIP 9308 Association SNV 3' UTR variant NM_001385218.1:c.*25A>G -
MY_SAMPLE chr20 6786464 BMP2 996153 Confers sensitivity SNV No consequences found BMP2-LINC01428:n.6786464A>G -
MY_SAMPLE chr20 3213247 ITPA 14747 Drug response SNV Intron variant NM_001324237.2:c.-214+21A>C -

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 v1.0.4

Workflow parameters

Key Value
snp True
sv True
mod False
str False
cnv False
bam demo_data/demo.bam
bed demo_data/demo.bed
ref demo_data/demo.fasta
basecaller_cfg dna_r10.4.1_e8.2_400bps_hac@v4.1.0
sample_name MY_SAMPLE
out_dir output
disable_ping False
help False
version False
threads 4
aws_image_prefix None
aws_queue None
mapula False
sv_benchmark False
sv_benchmark_vcf None
sv_benchmark_bed None
fast5_dir None
old_ref None
bam_min_coverage 20
downsample_coverage False
downsample_coverage_target 60
downsample_coverage_margin 1.1
depth_window_size 25000
basecaller dorado
basecaller_chunk_size 25
basecaller_args None
basecaller_basemod_threads 2
cuda_device cuda:all
ubam_map_threads 8
ubam_sort_threads 3
ubam_bam2fq_threads 1
fastq_only False
merge_threads 4
basecaller_model_path None
remora_model_path None
qscore_filter 10
remora_cfg None
dorado_ext fast5
annotation True
annotation_threads 8
clair3_model_path None
phase_vcf False
use_longphase True
use_longphase_intermediate True
ctg_name EMPTY
include_all_ctgs False
ref_pct_full 0.1
var_pct_full 0.7
GVCF False
snp_min_af 0.08
indel_min_af 0.15
vcf_fn EMPTY
min_contig_size 0
min_mq 5
min_cov 2
min_qual 2
refine_snp_with_sv True
tr_bed None
min_sv_length 30
min_read_support auto
min_read_support_limit 2
cluster_merge_pos 150
sniffles_args None
bin_size 500
modkit_args None
phase_mod False
force_strand False
modkit_threads 4
sex female
depth_intervals False
joint_phasing 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,min_read_support,min_read_support_limit,fastq_only
wf {'name': 'wf-human-variation', 'template_version': '195cab5', 'example_cmd': ['--bam wf-human-variation-demo/demo.bam', '--basecaller_cfg clair3:dna_r10.4.1_e8.2_400bps_hac_prom', '--mod', '--ref wf-human-variation-demo/demo.fasta', '--sample_name DEMO', '--snp', '--sv'], 'agent': None, 'e2l_base_tag': 'sha1b503961726c6e02b6b908297a9797db953b46a3', 'e2l_snp_tag': 'sha0d7e7e8e8207d9d23fdf50a34ceb577da364373e', 'e2l_sv_tag': 'shabc3ac908a14705f248cdf49f218956ec33e93ef9', 'e2l_mod_tag': 'shaa6e616571797d97ae2736c7ebdcb4613fe77f263', 'basecaller_container': 'dorado:sha1433bfc3146fd0dc94ad9648452364f2327cf1b0', 'cnv_tag': 'sha428cb19e51370020ccf29ec2af4eead44c6a17c2', 'str_tag': 'sha28799bc3058fa256c01c1f07c87f04e4ade1fcc1', 'snpeff_tag': 'sha4f289afaf754c7a3e0b9ffb6c0b5be0f89a5cf04', 'common_sha': 'sha0a6dc21fac17291f4acb2e0f67bcdec7bf63e6b7'}