Summary

This report contains visualisations of statistics that can help in understanding the results from the wf-human-variation workflow. Each section contains different plots or tables, and in general the results are broken down by sample. You can quickly jump to an individual section with the links in the header bar.

Metric Value Percentage
Reads 2,319
100.0%
Unmapped reads 0
0.0%
Bases 29,548,232
100.0%

Read statistics

Alignment statistics

This section displays the alignment statistics for the sample processed. The left plot shows the mapping accuracy (ranging from 0-100%) vs. the number of reads. The right plot shows the depth of sequencing vs. number of reads.

Mapping accuracy
Read coverage

Depth of coverage

This section illustrates the depth of coverage of the reference genomes. The plot shows coverage vs. genomic position (note that the coordinates on the x-axis are the positions along the concatenated reference including all reference sequences in the respective reference file).

Software versions

Name Version
mosdepth 0.3.3
bamstats 0.10.2

Workflow parameters

Key Value
help False
version False
disable_ping False
threads 4
aws_image_prefix None
aws_queue None
out_dir wf-human-variation
snp True
sv True
mod False
cnv False
str False
mapula False
sv_benchmark False
sv_benchmark_vcf None
sv_benchmark_bed None
fast5_dir None
bam snp_demo/chr6_chr20.bam
ref snp_demo/chr6_chr20.fasta
old_ref None
bed snp_demo/chr6_chr20.bed
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_cfg dna_r10.4.1_e8.2_400bps_sup@v4.1.0
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 4
clair3_model_path snp_demo/ont_r104_e81_sup_g5015
phase_vcf True
use_longphase True
use_longphase_intermediate True
sample_name SAMPLE
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': 'cw-ci', 'e2l_base_tag': 'sha0800eade05e4cbb75d45421633c78c4f6320b2f6', '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'}