Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

fix: replace total seq(samtools) with total reads (picard) in multiqc dna general stats #46

Merged
merged 2 commits into from
Oct 3, 2023
Merged

fix: replace total seq(samtools) with total reads (picard) in multiqc dna general stats #46

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
3fe896d
fix: replace total seq(samtools) with total reads (picard)
elleira Oct 3, 2023
2474add
docs: add general stats and some program version updates
elleira Oct 3, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
28 changes: 28 additions & 0 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -144,6 +144,30 @@ All results (as described in table below) are located in: `Results/{project}/{sa
| `SV/{sample}_manta_TN.bnd.aml.tsv` | `.tsv` file for excel containing breakends found by Manta (filtered), filtered for AML genes|


#### General Statistics - DNA
The general statistics table are ordered based on the sample order in `SampleSheet.csv`, this is done by renaming the samples in two steps using the script `sample_order_multiqc.py`. To toggle between "Sample Order" and "Sample Name" use the buttons just above General Stats header.

<br />

| Column Name | Origin | Comment |
| --- | --- | --- |
| M Reads | [Picard](https://broadinstitute.github.io/picard/) HSMetrics | Total number of reads in inputfile (`alignment/samtools_merge_bam/{sample}_{type}.bam`) |
| % Mapped| [Samtools stats](http://www.htslib.org/doc/samtools-stats.html) | Only reads on target (`config[reference][design_bed]`) |
| % Proper pairs| [Samtools stats](http://www.htslib.org/doc/samtools-stats.html) | Only reads on target (`config[reference][design_bed]`) |
| Average Quality | [Samtools stats](http://www.htslib.org/doc/samtools-stats.html) | Ratio between sum of base quality over total length. Only reads on target (`config[reference][design_bed]`) |
| Median | [Mosdepth](https://github.com/brentp/mosdepth) | Median Coverage over reference |
| >= 10X | [Mosdepth](https://github.com/brentp/mosdepth) | Fraction of reference with coverage over 10x |
| >= 30X | [Mosdepth](https://github.com/brentp/mosdepth) | Fraction of reference with coverage over 30x |
| >=50X |[Mosdepth](https://github.com/brentp/mosdepth) | Fraction of reference with coverage over 50x |
| Error sex check |[Peddy](https://github.com/brentp/peddy)| Result of sex check based on sex in samplesheet |
| Predicted sex sex check |[Peddy](https://github.com/brentp/peddy)| |
| Bases on Target | [Picard](https://broadinstitute.github.io/picard/) HSMetrics | Bases inside the capture design (`config[reference][design_intervals]`) |
| Fold80 |[Picard](https://broadinstitute.github.io/picard/) HSMetrics | The fold over-coverage necessary to raise 80% of bases in "non-zero-cvg" targets to the mean coverage level in those targets (`config[reference][design_intervals]`) |
| % Dups | [Picard](https://broadinstitute.github.io/picard/) DuplicationMetrics | |
| Mean Insert Size | [Picard](https://broadinstitute.github.io/picard/) InsertSizeMetrics | |
| Target Bases with zero coverage [%] | [Picard](https://broadinstitute.github.io/picard/) HSMetrics | Percent target (`config[reference][design_intervals]`) bases with 0 coverage |
| % Adapter | [fastp](https://github.com/OpenGene/fastp) | |

### Program versions

default container: `docker://hydragenetics/common:0.1.9`
Expand All @@ -156,9 +180,12 @@ default container: `docker://hydragenetics/common:0.1.9`
| fastp | 0.20.1 | `docker://hydragenetics/fastp:0.20.1` |
| FastQC | 0.11.9 | `docker://hydragenetics/fastqc:0.11.9` |
| FusionCatcher | 1.33 | `docker://blcdsdockerregistry/fusioncatcher:1.33` |
| GATK | 4.2.2.0 | `docker://hydragenetics/gatk4:4.2.2.0` |
| Manta | 1.6.0 | `docker://hydragenetics/manta:1.6.0` |
| Mosdepth | 0.3.2 | `docker://hydragenetics/mosdepth:0.3.2` |
| MultiQC | 1.11 | `docker://hydragenetics/multiqc:1.11` |
| Parabricks | 4.0.0-1 | `docker://nvcr.io/nvidia/clara/clara-parabricks:4.0.0-1` |
| Peddy | 0.4.8 | `docker://hydragenetics/peddy:0.4.8` |
| Picard | 2.25.0 | `docker://hydragenetics/picard:2.25.0` |
| Pindel | 0.2.5b9 | `docker://hydragenetics/pindel:0.2.5b9` |
| RSeQC | 4.0.0 | `docker://hydragenetics/rseqc:4.0.0` |
Expand All @@ -168,6 +195,7 @@ default container: `docker://hydragenetics/common:0.1.9`
| SPRING | 1.0.1 | `docker://hydragenetics/spring:1.0.1` |
| STAR | 2.7.10a | `docker://hydragenetics/star:2.7.10a` |
| STAR-Fusion | 1.10.1 | `docker://trinityctat/starfusion:1.10.1` |
| svdb | 2.6.0 | `docker://hydragenetics/svdb:2.6.0` |
| VEP | 105 | `docker://hydragenetics/vep:105` |

## :judge: Rule Graph Parabricks version
Expand Down
6 changes: 4 additions & 2 deletions config/multiqc_dna_config.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -74,14 +74,15 @@ table_columns_visible:
PCT_30X: False
PCT_TARGET_BASES_30X: False
FOLD_ENRICHMENT: False
TOTAL_READS: True
Samtools:
error_rate: False
non-primary_alignments: False
reads_mapped: True
reads_mapped: False
reads_mapped_percent: True
reads_properly_paired_percent: True
reads_MQ0_percent: False
raw_total_sequences: True
raw_total_sequences: False

# Patriks plug in, addera egna columner till general stats
multiqc_cgs:
Expand Down Expand Up @@ -149,6 +150,7 @@ table_columns_placement:
predicted_sex_sex_check: 702
family_id: 703
Picard:
TOTAL_READS: 500
PCT_SELECTED_BASES: 801
FOLD_80_BASE_PENALTY: 802
PCT_PF_READS_ALIGNED: 888
Expand Down
Loading