STR genotyping results

The tabs below contain short tandem repeat (STR) expansion plots for each repeat genotyped in the sample. The coloured boxes denote the normal and pathogenic ranges of repeat numbers, and the triangles denote the median number of repeats in each allele.

FragileX (FMR1)

There are no pre-mutation results detected.

Fraxe (AFF2)

SBMA (AR)

Summary of STR genotyping results

The table below summarises the repeat expansions genotyped in this sample.

Gene Repeat unit Chromosome Start End No. reads covering locus Allele 1 repeat number* Allele 1 size (bp)* Allele 2 repeat number* Allele 2 size (bp)*
AR GCA chrX 67545316 67545385 21 20.0 60.0 16.0 48.0
FMR1 GGC chrX 147912050 147912110 16 930.3 2791.0 32.3 97.0
AFF2 GCC chrX 148500631 148500691 18 29.3 88.0 22.3 67.0

* Median values

Repeat number key:

Normal Pre-mutation Mutation

STR content

The tabs below contain short tandem repeat (STR) expansion plots for each repeat genotyped in the sample. These plots display repeat units and interruptions for each supporting read. Hover over the coloured bars to view more detailed information for each read: the read identifier, position of each repeat unit within the read, and the sequence content. Please note, repeat content plots are displayed only for those repeats which fall in the 'Mutation' or 'Pre-mutation' ranges.

FragileX (FMR1)

Repeat Unit: CGG

There are no pre-mutation results detected.

Quality Control Data

Software versions

Name Version
pysam 0.21.0
samtools 1.17
straglr-genotype 1.4.1
stranger 0.8.1

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 False
sv False
mod False
cnv False
str True
mapula False
sv_benchmark False
sv_benchmark_vcf None
sv_benchmark_bed None
fast5_dir None
bam demo_data/demo.bam
ref demo_data/GCA_000001405.15_GRCh38_no_alt_analysis_set.fa.gz
old_ref None
bed None
bam_min_coverage 1e-05
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 False
clair3_model_path None
phase_vcf False
use_longphase True
use_longphase_intermediate True
sample_name demo
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': 'shaeedb131a939d3eea2f9bd4dbecec805c0fa20bdb', 'basecaller_container': 'dorado:sha1433bfc3146fd0dc94ad9648452364f2327cf1b0', 'cnv_tag': 'sha428cb19e51370020ccf29ec2af4eead44c6a17c2', 'str_tag': 'sha28799bc3058fa256c01c1f07c87f04e4ade1fcc1', 'snpeff_tag': 'sha4f289afaf754c7a3e0b9ffb6c0b5be0f89a5cf04', 'common_sha': 'sha91452ece4f647f62b32dac3a614635a6f0d7f8b5'}