From VCFs to SNP distance matrix
Version 1

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Workflow Type: Galaxy

Galaxy workflow

SEEK ID: https://dev.workflowhub.eu/workflows/1009?version=1

Inputs

ID Name Description Type
Collection of VCFs to analyze #main/Collection of VCFs to analyze n/a
  • array containing
    • File
Reference genome of the MTBC ancestor #main/Reference genome of the MTBC ancestor n/a
  • File

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
  • File
_anonymous_output_1 #main/_anonymous_output_1 n/a
  • File
_anonymous_output_2 #main/_anonymous_output_2 n/a
  • File
_anonymous_output_3 #main/_anonymous_output_3 n/a
  • File
_anonymous_output_4 #main/_anonymous_output_4 n/a
  • File

Version History

2 (earliest) Created 22nd Apr 2024 at 11:19 by Helena Rasche

Added/updated 3 files


Open master 7552cf5
help Creators and Submitter
Creators
Not specified
Submitter
Tools
COMBAT-TB Workbench
BCFtools
License
Creative Commons Attribution 4.0 International
Activity

Views: 23

Created: 22nd Apr 2024 at 11:19

Last updated: 22nd Apr 2024 at 11:19

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