From VCFs to SNP distance matrix
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Download RO-CrateGiven a set of VCF files and the reference genome used to do the mapping and SNP calling, create a multifasta file containing the genomes of all samples and calculate the matrix of pairwise SNP distances
Associated Tutorial
This workflows is part of the tutorial From VCFs to SNP distance matrix, available in the GTN
Thanks to...
Tutorial Author(s): Galo A. Goig, Daniela Brites, Christoph Stritt
Tutorial Contributor(s): Wolfgang Maier
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Collection of VCFs to analyze | #main/Collection of VCFs to analyze | n/a |
|
| Reference genome of the MTBC ancestor | #main/Reference genome of the MTBC ancestor | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 2 | Filter TB variants | We will ensure at this step that variants to build the MSA are fixed variants and that we low-confidence filter repetitive regions of the MTB genome toolshed.g2.bx.psu.edu/repos/iuc/tb_variant_filter/tb_variant_filter/0.1.3+galaxy0 |
| 3 | Generate the complete genome of each of the samples | The complete genome of each of the samples is generated by inserting the SNPs defined in the respective VCF in the reference genome that was used for mapping and SNP calling toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.9+galaxy2 |
| 4 | Concatenate genomes to build a MSA | All genomes are concatenated in a single multifasta file. Because all o them have the same length, this may be seen as a multiple sequence alignment. toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1 |
| 5 | Keep only variable positions | Discard invariant positions from the MSA to simplify the file so only contains positions with at least one SNP in at least one strain. toolshed.g2.bx.psu.edu/repos/iuc/snp_sites/snp_sites/2.5.1+galaxy0 |
| 6 | Calculate SNP distances | From the MSA. Calculate pairwise SNP distances between samples. toolshed.g2.bx.psu.edu/repos/iuc/snp_dists/snp_dists/0.6.3+galaxy0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| {input_file} | #main/{input_file} | n/a |
|
| _anonymous_output_1 | #main/_anonymous_output_1 | n/a |
|
| _anonymous_output_2 | #main/_anonymous_output_2 | n/a |
|
| _anonymous_output_3 | #main/_anonymous_output_3 | n/a |
|
| _anonymous_output_4 | #main/_anonymous_output_4 | n/a |
|
Version History
1.0 (latest) Created 16th Jul 2024 at 14:24 by Helena Rasche
Added/updated 4 files
Open
master058351f
2.0 (earliest) Created 25th Jun 2024 at 11:22 by Helena Rasche
Added/updated 4 files
Frozen
2.05a40a06
Creators and Submitter
Views: 228 Downloads: 83
Created: 25th Jun 2024 at 11:22
Last updated: 25th Jun 2024 at 11:22
AttributionsNone
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