At a glance

This report contains visualisations of alignment statistics for paired tumor/normal samples that can help in understanding the results from the wf-somatic-variation. Each section contains different plots or tables, and in general the results are broken down by sample or the reference file to which alignments were made. You can quickly jump to an individual section with the links in the header bar.

Tumor Total Reads

13,525

Normal Total Reads

7,154

Tumor Read N50

30,722 bp

Normal Read N50

24,108 bp

Tumor mean coverage

3.406x

Normal mean coverage

1.454x

Base statistics

The aligned bam files have been tested for coverage thresholds of 0.0x for the tumor and 0.0x for the normal sequences.

Sample Type Total Reads Median Read Length Read N50 Min chrom. coverage Mean chrom. coverage Max chrom. coverage Pass threshold
SAMPLE Tumor 13525 10191 30722 3.406 3.406 3.406 PASS
SAMPLE Normal 7154 8171 24108 1.454 1.454 1.454 PASS

Read length distribution

Red: read N50; Yellow: mean length; Purple: median length.

Mean read quality

Yellow: mean length; Purple: median length.

Alignment statistics

Type ref sample_name total primary secondary supplementary qcfail duplicate Status filename
Tumor chr20 SAMPLE 14990 13525 701 764 0 0 Mapped flagstat_tumor.tsv
Tumor * SAMPLE 0 0 0 0 0 0 Unmapped flagstat_tumor.tsv
Normal chr20 SAMPLE 7949 7154 392 403 0 0 Mapped flagstat_normal.tsv
Normal * SAMPLE 0 0 0 0 0 0 Unmapped flagstat_normal.tsv

Yellow: mean length; Purple: median length.

The distribution is truncated to show the range between 80-100%.

Coverage

Depth of coverage computed by mosdepth. The dashed line shows the total mean coverage.

Software versions

Name Version
python 3.8.17
minimap2 2.24-r1122
samtools 1.18
fastcat 0.13.2
mosdepth 0.3.3
ezcharts 0.6.4
pysam 0.21.0
bgzip 1.18
tabix 1.18

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'}