Sep 21, 2020
nf-100GMX-variant-summarizer
- 1Instituto Nacional de Medicina Genómica (INMEGEN)
- Whole genome variation in 27 Mexican indigenous populations, demographic and biomedical insights
External link: https://github.com/Iaguilaror/nf-100GMX-variant-summarizer
Protocol Citation: Israel Aguilar Ordoñez 2020. nf-100GMX-variant-summarizer. protocols.io https://dx.doi.org/10.17504/protocols.io.bkv6kw9e
Manuscript citation:
Aguilar-Ordoñez I, Pérez-Villatoro F, García-Ortiz H, Barajas-Olmos F, Ballesteros-Villascán J, González-Buenfil R, Fresno C, Garcíarrubio A, Fernández-López JC, Tovar H, Hernández-Lemus E, Orozco L, Soberón X, Morett E (2021) Whole genome variation in 27 Mexican indigenous populations, demographic and biomedical insights. PLoS ONE 16(4): e0249773. doi: 10.1371/journal.pone.0249773
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: September 05, 2020
Last Modified: September 21, 2020
Protocol Integer ID: 41630
Abstract
Nextflow pipeline used to count variants for the 100GMX project
'nf-100GMX-variant-summarizer' is a pipeline tool that counts variants in a VEPextended annotated VCF file.
This pipeline generates 3 outputs:
1) a TSV file with the total number of SNV and indels
2) a TSV file with per sample counts for variants of type SNV, indel, novel, worldwide singletons, clinvar, gwascat and pharmgkb
3) a PDF file with the number of discernible variants in sample groups of interest.
Important note: input file must be previously annotated by https://github.com/Iaguilaror/nf-VEPextended
Guidelines
Installation
Download nf-100GMX-variant-summarizer from Github repository:
git clone https://github.com/Iaguilaror/nf-100GMX-variant-summarizer
Compatible OS*:
* nf-100GMX-variant-summarizer may run in other UNIX based OS and versions, but testing is required.
Software Requirements:
Software
bcftools
NAME
Software
htslib
NAME
Software
filter_vep
NAME
Software
Nextflow
NAME
Software
R
NAME
Materials
Pipeline Inputs
- A compressed vcf file with extension '.vcf.gz'; the VCF must be previously annotated withhttps://github.com/Iaguilaror/nf-VEPextended
Example line(s):
##fileformat=VCFv4.2 #CHROM POS ID REF ALT QUAL FILTER INFO chr21 5101724 . G A . PASS AC=1;AF=0.00641;AN=152;DP=903;ANN=A|intron_variant|MODIFIER|GATD3B|ENSG00000280071|Transcript|ENST00000624810.3|protein_coding||4/5|ENST00000624810.3:c.357+19987C>T|||||||||-1|cds_start_NF&cds_end_NF|SNV|HGNC|HGNC:53816||5|||ENSP00000485439||A0A096LP73|UPI0004F23660|||||||chr21:g.5101724G>A||||||||||||||||||||||||||||2.079|0.034663|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| chr21 5102165 rs1373489291 G T . PASS AC=1;AF=0.00641;AN=140;DP=853;ANN=T|intron_variant|MODIFIER|GATD3B|ENSG00000280071|Transcript|ENST00000624810.3|protein_coding||4/5|ENST00000624810.3:c.357+19546C>A|||||||rs1373489291||-1|cds_start_NF&cds_end_NF|SNV|HGNC|HGNC:53816||5|||ENSP00000485439||A0A096LP73|UPI0004F23660|||||||chr21:g.5102165G>T||||||||||||||||||||||||||||5.009|0.275409||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
- *.tsv: A metadata file, relating every sample ID (as registered in the VCF file) and a sample group in column format.
Example line(s):
sample group
SM-3MG5L Chinanteco
SM-3MG5F Chocholteco
SM-3MG46 Kanjobal
Before start
Test
To test nf-100GMX-variant-summarizer's execution using test data, run:
./runtest.sh
Your console should print the Nextflow log for the run, once every process has been submitted, the following message will appear:
======
VCF summarizer: Basic pipeline TEST SUCCESSFUL
======
nf-100GMX-variant-summarizer results for test data should be in the following file:
nf-100GMX-variant-summarizer/test/results/VCFsummarizer-results
Usage
To run nf-100GMX-variant-summarizer go to the pipeline directory and execute:
nextflow run summarize-vcf.nf --vcffile <path to input 1> --metadata <path to input 2> --nsamples <integer> --group_minaf <numeric> --outgroup_maxaf <numeric> [--output_dir path to results ]
For information about options and parameters, run:
nextflow run summarize-vcf.nf --help
Branch A
Branch A
Project Counts
Note
a) Count samples and raw stats for all samples.
b) Give the total counts data.
Branch B
Branch B
No filter counts
Note
a) Filter variants that are not in ClinVar, GWAS Catalog or PGKB.
b) Give the total counts data.
Dependencies:
- final-counter.R
Software
bcftools
NAME
Novel counts
Note
a) Filter variants without a rsID.
b) Give the total counts data.
Dependencies:
- final-counter.R
Software
bcftools
NAME
Worldwide singletons counts
Note
a) Filter variants that are singletons.
b) Keep variants that have not frequencies in another population.
Dependencies:
- final-counter.R
Software
bcftools
NAME
Software
filter_vep
NAME
ClinVar counts
Note
a) Filter variants harbored in CinVar.
b) Give the total counts data.
Dependencies:
- final-counter.R
Software
filter_vep
NAME
Software
bcftools
NAME
GWASCatalog counts
Note
a) Filter variants harbored in GWAS Catalog.
b) Give the total counts data.
Dependencies:
- final-counter.R
Software
bcftools
NAME
Software
filter_vep
NAME
PGKB counts
Note
a) Filter variants harbored in Pharm GKB.
b) Give the total counts data.
Dependencies:
- final-counter.R
Software
bcftools
NAME
Software
filter_vep
NAME
Merge tables
Merge tables of counted data.
Dependencies:
- merger.R
Branc C
Branc C
Define groups
Note
a) Count samples per group.
b) Join in a file samples per group.
Dependencies:
NONE
Select world rare
Note
a) Filter variants according AF in gnomAD populations and NatMex.
Dependencies:
Software
filter_vep
NAME
Extract discernible VCF
Note
a) Extract variants in other samples.
b) Extract variants in local samples.
c) Extract exclusive variants.
Dependencies:
Software
bcftools
NAME
Count and Plot
Note
a) Count the number of discernible variants per group and type in a TSV file.
b) Plot number of discernible variants per group and type.
Dependencies:
Software
bcftools
NAME
- plotter.R