RO-Crate Summary
RO-Crate ID
ark:59853/rocrate-variant-calling-on-three-sequenced-sampl-68f3c95
Version
1.0
Release date
2026-09-11T13:35:02.543766-04:00
Description
Reads from three samples aligned to the reference with bwa-mem, sorted and indexed with samtools, and jointly called with bcftools; a Snakemake run captured as an EVI RO-Crate.
Authors
Example Researcher
Keywords
snakemake, variant calling, bwa, bcftools, genomics
Contents 44 entities
| Name | Description | Format | Size | Access | Date | Identifier |
|---|---|---|---|---|---|---|
| config.yaml | Snakemake configuration file 'config.yaml' for this run | yaml | 375 B | Available | 2026-09-11 | ark:59853/dataset-config-yaml-b5106b5 |
| genome.fa | Input file 'data/genome.fa' used by the Snakemake workflow run | fasta | 234.1 KB | Available | 2026-09-11 | ark:59853/dataset-genome-fa-f891ca0 |
| genome.fa.amb | Input file 'data/genome.fa.amb' used by the Snakemake workflow run | amb | 2.6 KB | Available | 2026-09-11 | ark:59853/dataset-genome-fa-amb-c2df282 |
| genome.fa.ann | Input file 'data/genome.fa.ann' used by the Snakemake workflow run | ann | 83 B | Available | 2026-09-11 | ark:59853/dataset-genome-fa-ann-936b248 |
| genome.fa.bwt | Input file 'data/genome.fa.bwt' used by the Snakemake workflow run | bwt | 230.3 KB | Available | 2026-09-11 | ark:59853/dataset-genome-fa-bwt-0a9c7e3 |
| genome.fa.pac | Input file 'data/genome.fa.pac' used by the Snakemake workflow run | ns-proxy-autoconfig | 57.6 KB | Available | 2026-09-11 | ark:59853/dataset-genome-fa-pac-28b255e |
| genome.fa.sa | Input file 'data/genome.fa.sa' used by the Snakemake workflow run | sa | 115.2 KB | Available | 2026-09-11 | ark:59853/dataset-genome-fa-sa-90bdcc1 |
| A.fastq | Input file 'data/samples/A.fastq' used by the Snakemake workflow run | fastq | 5.8 MB | Available | 2026-09-11 | ark:59853/dataset-a-fastq-d4611b6 |
| B.fastq | Input file 'data/samples/B.fastq' used by the Snakemake workflow run | fastq | 5.8 MB | Available | 2026-09-11 | ark:59853/dataset-b-fastq-7ed58c5 |
| C.fastq | Input file 'data/samples/C.fastq' used by the Snakemake workflow run | fastq | 5.8 MB | Available | 2026-09-11 | ark:59853/dataset-c-fastq-bef0063 |
| all.vcf | File 'results/calls/all.vcf' produced by the Snakemake workflow run | vcf | 111.6 KB | Available | 2026-09-11 | ark:59853/dataset-all-vcf-637cf3e |
| variant_summary.tsv | File 'results/calls/variant_summary.tsv' produced by the Snakemake workflow run | tsv | 14.6 KB | Available | 2026-09-11 | ark:59853/dataset-variant-summary-tsv-71310c4 |
| A.bam | File 'results/mapped/A.bam' produced by the Snakemake workflow run | bam | — | No link | 2026-09-11 | ark:59853/dataset-a-bam-016e31c |
| B.bam | File 'results/mapped/B.bam' produced by the Snakemake workflow run | bam | — | No link | 2026-09-11 | ark:59853/dataset-b-bam-6b7c70e |
| C.bam | File 'results/mapped/C.bam' produced by the Snakemake workflow run | bam | — | No link | 2026-09-11 | ark:59853/dataset-c-bam-3e0f2ac |
| quals.svg | File 'results/plots/quals.svg' produced by the Snakemake workflow run | svg | 32.4 KB | Available | 2026-09-11 | ark:59853/dataset-quals-svg-81b3cdb |
| A.bam | File 'results/sorted/A.bam' produced by the Snakemake workflow run | bam | 2.2 MB | Available | 2026-09-11 | ark:59853/dataset-a-bam-c0907f3 |
| A.bam.bai | File 'results/sorted/A.bam.bai' produced by the Snakemake workflow run | binary | 344 B | Available | 2026-09-11 | ark:59853/dataset-a-bam-bai-9ebeb4d |
| B.bam | File 'results/sorted/B.bam' produced by the Snakemake workflow run | bam | 2.2 MB | Available | 2026-09-11 | ark:59853/dataset-b-bam-cbee9ae |
| B.bam.bai | File 'results/sorted/B.bam.bai' produced by the Snakemake workflow run | binary | 344 B | Available | 2026-09-11 | ark:59853/dataset-b-bam-bai-6a20e1e |
| C.bam | File 'results/sorted/C.bam' produced by the Snakemake workflow run | bam | 2.2 MB | Available | 2026-09-11 | ark:59853/dataset-c-bam-7ccb833 |
| C.bam.bai | File 'results/sorted/C.bam.bai' produced by the Snakemake workflow run | binary | 344 B | Available | 2026-09-11 | ark:59853/dataset-c-bam-bai-39648ed |
Nothing in this tab matches your filter.
| Name | Description | Format | Size | Access | Date | Identifier |
|---|---|---|---|---|---|---|
| Snakefile | Snakemake workflow definition 'Snakefile' for this run | snakemake | — | Available | ark:59853/software-snakefile-68f3c95 | |
| Snakemake | Snakemake workflow management system (https://snakemake.github.io/) | python | — | Access / download | ark:59853/software-snakemake-059f146 | |
| bcftools_call | (bcftools mpileup {params.mpileup} -f {input.genome} {input.bam} | bcftools call {params.call} -o… | snakemake | — | Available | ark:59853/software-bcftools-call-7c9ed78 | |
| bwa_map | bwa mem -t {threads} -R '{params.read_group}' {input.genome} {input.reads} 2> {log} | samtools view… | snakemake | — | Available | ark:59853/software-bwa-map-0bcb380 | |
| plot_quals | """Plot the quality-score distribution of the called variants. Snakemake runs this with a… | python | — | Available | ark:59853/software-plot-quals-d88cf8f | |
| samtools_index | samtools index {input} | snakemake | — | Available | ark:59853/software-samtools-index-b6cd086 | |
| samtools_sort | samtools sort -T results/sorted/{wildcards.sample} -O bam {input} > {output} 2> {log} | snakemake | — | Available | ark:59853/software-samtools-sort-65f7fb4 | |
| variant_summary | (printf 'chrom\tpos\tref\talt\tquality\tdepth\n'; bcftools query -f… | snakemake | — | Available | ark:59853/software-variant-summary-aea5e1b |
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| Name | Description | Date | Identifier | Details | |||||||||||||||||||||||||||||||||||||||||||||
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| Snakemake workflow run of 'Snakefile' | Execution of the Snakemake workflow 'Snakefile', reconstructed post-hoc from Snakemake's… | 2026-09-11 | ark:59853/computation-variant-calling-on-three-sequenced-sampl-f05a611 | ||||||||||||||||||||||||||||||||||||||||||||||
| Inputs 9
Outputs 2
Software used
Command
snakemake |
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| bcftools_call | Snakemake job for rule 'bcftools_call' | 2026-09-11 | ark:59853/computation-bcftools-call-c76dde6 | ||||||||||||||||||||||||||||||||||||||||||||||
| Inputs 7
Outputs 1
Software used
Parameters
'-d 250 -a AD,DP' · '-mv -Ov' Command
(bcftools mpileup -d 250 -a AD,DP -f data/genome.fa results/sorted/A.bam results/sorted/B.bam results/sorted/C.bam | bcftools call -mv -Ov -o results/calls/all.vcf) 2> logs/bcftools_call/all.log |
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| bwa_map (sample=A) | Snakemake job for rule 'bwa_map' with wildcards {'sample': 'A'} | 2026-09-11 | ark:59853/computation-bwa-map-sample-a-9183688 | ||||||||||||||||||||||||||||||||||||||||||||||
| Inputs 7
Outputs 1
Software used
Parameters
'@RG\\tID:A\\tSM:A\\tPL:ILLUMINA' Command
bwa mem -t 2 -R '@RG\tID:A\tSM:A\tPL:ILLUMINA' data/genome.fa data/samples/A.fastq 2> logs/bwa_map/A.log | samtools view -Sb - > results/mapped/A.bam |
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| bwa_map (sample=B) | Snakemake job for rule 'bwa_map' with wildcards {'sample': 'B'} | 2026-09-11 | ark:59853/computation-bwa-map-sample-b-5025f30 | ||||||||||||||||||||||||||||||||||||||||||||||
| Inputs 7
Outputs 1
Software used
Parameters
'@RG\\tID:B\\tSM:B\\tPL:ILLUMINA' Command
bwa mem -t 2 -R '@RG\tID:B\tSM:B\tPL:ILLUMINA' data/genome.fa data/samples/B.fastq 2> logs/bwa_map/B.log | samtools view -Sb - > results/mapped/B.bam |
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| bwa_map (sample=C) | Snakemake job for rule 'bwa_map' with wildcards {'sample': 'C'} | 2026-09-11 | ark:59853/computation-bwa-map-sample-c-c80046e | ||||||||||||||||||||||||||||||||||||||||||||||
| Inputs 7
Outputs 1
Software used
Parameters
'@RG\\tID:C\\tSM:C\\tPL:ILLUMINA' Command
bwa mem -t 2 -R '@RG\tID:C\tSM:C\tPL:ILLUMINA' data/genome.fa data/samples/C.fastq 2> logs/bwa_map/C.log | samtools view -Sb - > results/mapped/C.bam |
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| plot_quals | Snakemake job for rule 'plot_quals' | 2026-09-11 | ark:59853/computation-plot-quals-8e2e10d | ||||||||||||||||||||||||||||||||||||||||||||||
| Inputs 1
Outputs 1
Software used
Command
script: scripts/plot_quals.py |
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| samtools_index (sample=A) | Snakemake job for rule 'samtools_index' with wildcards {'sample': 'A'} | 2026-09-11 | ark:59853/computation-samtools-index-sample-a-13242d2 | ||||||||||||||||||||||||||||||||||||||||||||||
| Inputs 1
Outputs 1
Software used
Command
samtools index results/sorted/A.bam |
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| samtools_index (sample=B) | Snakemake job for rule 'samtools_index' with wildcards {'sample': 'B'} | 2026-09-11 | ark:59853/computation-samtools-index-sample-b-f89dac4 | ||||||||||||||||||||||||||||||||||||||||||||||
| Inputs 1
Outputs 1
Software used
Command
samtools index results/sorted/B.bam |
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| samtools_index (sample=C) | Snakemake job for rule 'samtools_index' with wildcards {'sample': 'C'} | 2026-09-11 | ark:59853/computation-samtools-index-sample-c-d37cbd8 | ||||||||||||||||||||||||||||||||||||||||||||||
| Inputs 1
Outputs 1
Software used
Command
samtools index results/sorted/C.bam |
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| samtools_sort (sample=A) | Snakemake job for rule 'samtools_sort' with wildcards {'sample': 'A'} | 2026-09-11 | ark:59853/computation-samtools-sort-sample-a-3bd01fd | ||||||||||||||||||||||||||||||||||||||||||||||
| Inputs 1
Outputs 1
Software used
Command
samtools sort -T results/sorted/A -O bam results/mapped/A.bam > results/sorted/A.bam 2> logs/samtools_sort/A.log |
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| samtools_sort (sample=B) | Snakemake job for rule 'samtools_sort' with wildcards {'sample': 'B'} | 2026-09-11 | ark:59853/computation-samtools-sort-sample-b-74d837f | ||||||||||||||||||||||||||||||||||||||||||||||
| Inputs 1
Outputs 1
Software used
Command
samtools sort -T results/sorted/B -O bam results/mapped/B.bam > results/sorted/B.bam 2> logs/samtools_sort/B.log |
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| samtools_sort (sample=C) | Snakemake job for rule 'samtools_sort' with wildcards {'sample': 'C'} | 2026-09-11 | ark:59853/computation-samtools-sort-sample-c-1828156 | ||||||||||||||||||||||||||||||||||||||||||||||
| Inputs 1
Outputs 1
Software used
Command
samtools sort -T results/sorted/C -O bam results/mapped/C.bam > results/sorted/C.bam 2> logs/samtools_sort/C.log |
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| variant_summary | Snakemake job for rule 'variant_summary' | 2026-09-11 | ark:59853/computation-variant-summary-d29c059 | ||||||||||||||||||||||||||||||||||||||||||||||
| Inputs 1
Outputs 1
Software used
Command
(printf 'chrom\tpos\tref\talt\tquality\tdepth\n'; bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%QUAL\t%INFO/DP\n' results/calls/all.vcf) > results/calls/variant_summary.tsv |
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| Name | Description | Identifier | Properties | |||||||||||||||||||||
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| Schema for variant_summary.tsv | Schema inferred from the tsv file 'results/calls/variant_summary.tsv' by… | ark:59853/schema-variant-summary-tsv-ec080af | ||||||||||||||||||||||
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