jvarkit

MsaToVcf

Getting a VCF file from a CLUSTAW or a FASTA alignment.

DEPRECATED

use https://github.com/sanger-pathogens/snp_sites

Usage

This program is now part of the main jvarkit tool. See jvarkit for compiling.

Usage: java -jar dist/jvarkit.jar msa2vcf  [options] Files

Usage: msa2vcf [options] Files
  Options:
    -a, --allsites
      print all sites
      Default: false
    --bcf-output
      If this program writes a VCF to a file, The format is first guessed from 
      the file suffix. Otherwise, force BCF output. The current supported BCF 
      version is : 2.1 which is not compatible with bcftools/htslib (last 
      checked 2019-11-15)
      Default: false
    -c, --consensus
      use this sequence as CONSENSUS
    -f, --fasta
      save computed fasta sequence in this file.
    --generate-vcf-md5
      Generate MD5 checksum for VCF output.
      Default: false
    -m, --haploid
      haploid output
      Default: false
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -N, --ignore-n-bases
      ignore, to the extent possible N-bases in the reads.
      Default: false
    -o, --output
      Output file. Optional . Default: stdout
    -R, --reference_contig_name
      reference name used for the CHROM column. Optional
      Default: chrUn
    --version
      print version and exit

Keywords

• vcf
• snp
• msa
• alignment

See also in Biostars

• https://www.biostars.org/p/94573

Creation Date

20151226

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/msa2vcf/MsaToVcf.java

Contribute

• Issue Tracker: http://github.com/lindenb/jvarkit/issues
• Source Code: http://github.com/lindenb/jvarkit

License

The project is licensed under the MIT license.

Citing

Should you cite msa2vcf ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md

The current reference is:

http://dx.doi.org/10.6084/m9.figshare.1425030

Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030

Deprecated: use https://github.com/sanger-pathogens/snp_sites , though some people told me they still use it for misc reasons.

Motivation

Getting a VCF file from a CLUSTAW alignment. See also http://www.biostars.org/p/94573/

input is a clustalw file like: https://github.com/biopython/biopython/blob/master/Tests/Clustalw/opuntia.aln

Cited-in

• ‘Differential distribution of Neandertal genomic signatures in human mitochondrial haplogroups’. 2017. Renata C Ferreira, Camila R Rodrigues, James R Broach, View ORCID ProfileMarcelo RS Briones. doi: https://doi.org/10.1101/190363
• ‘Pleiotropic effects of regulatory variation in tan result in correlation of two pigmentation traits in Drosophila melanogaster’. 2018. Molecular Ecology. Lukas Endler, Jean-Michel Gibert, Viola Nolte, Christian Schlotterer. doi: 10.1111/mec.14781
• ‘Two key events associated with a transposable element burst occurred during rice domestication’ https://doi.org/10.1101/405290
• ‘Tracking the origin of two genetic components associated with transposable element bursts in domesticated rice’. Nature Communicationsvolume 10, Article number: 641 (2019) https://www.nature.com/articles/s41467-019-08451-3
• ‘Predicting antimicrobial resistance in Pseudomonas aeruginosa with machine learning-enabled molecular diagnostics’. EMBO Mol Med (2020)e10264https://doi.org/10.15252/emmm.201910264
• Xi, L., Sun, Y., Xu, T., Wang, Z., Chiu, M. Y., Plouviez, S., Jollivet, D., & Qiu, J.-W. (2022). Phylogenetic divergence and population genetics of the hydrothermal vent annelid genus Hesiolyra along the East Pacific Rise: Reappraisal using multi-locus data. Diversity and Distributions, 00, 1-15. https://doi.org/10.1111/ddi.13653
• Yu-Qian Qin, Chu-Yun Yang, Ze-Long Nie, Jun Wen, Ying Meng,.Phylogenomics and divergence pattern of Polygonatum (Asparagaceae: Polygonateae) in the north temperate region,.Molecular Phylogenetics and Evolution,.2023,.107962,.ISSN 1055-7903,.https://doi.org/10.1016/j.ympev.2023.107962.
• Marshall VA, Cornejo Castro EM, Goodman CA, Labo N, Liu I, Fisher NC, et al. (2024) Sequencing of Kaposi s Sarcoma Herpesvirus (KSHV) genomes from persons of diverse ethnicities and provenances with KSHV-associated diseases demonstrate multiple infections, novel polymorphisms, and low intra-host variance. PLoS Pathog 20(7): e1012338. https://doi.org/10.1371/journal.ppat.1012338

Example

$ curl https://raw.github.com/biopython/biopython/master/Tests/Clustalw/opuntia.aln

CLUSTAL W (1.81) multiple sequence alignment


gi|6273285|gb|AF191659.1|AF191      TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAA
gi|6273284|gb|AF191658.1|AF191      TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAA
gi|6273287|gb|AF191661.1|AF191      TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAA
gi|6273286|gb|AF191660.1|AF191      TATACATAAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAA
gi|6273290|gb|AF191664.1|AF191      TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAA
gi|6273289|gb|AF191663.1|AF191      TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAA
gi|6273291|gb|AF191665.1|AF191      TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAA
                                    ******* **** *************************************

gi|6273285|gb|AF191659.1|AF191      TATATA----------ATATATTTCAAATTTCCTTATATACCCAAATATA
gi|6273284|gb|AF191658.1|AF191      TATATATA--------ATATATTTCAAATTTCCTTATATACCCAAATATA
gi|6273287|gb|AF191661.1|AF191      TATATA----------ATATATTTCAAATTTCCTTATATATCCAAATATA
gi|6273286|gb|AF191660.1|AF191      TATATA----------ATATATTTATAATTTCCTTATATATCCAAATATA
gi|6273290|gb|AF191664.1|AF191      TATATATATA------ATATATTTCAAATTCCCTTATATATCCAAATATA
gi|6273289|gb|AF191663.1|AF191      TATATATATA------ATATATTTCAAATTCCCTTATATATCCAAATATA
gi|6273291|gb|AF191665.1|AF191      TATATATATATATATAATATATTTCAAATTCCCTTATATATCCAAATATA
                                    ******          ********  **** ********* *********

gi|6273285|gb|AF191659.1|AF191      AAAATATCTAATAAATTAGATGAATATCAAAGAATCCATTGATTTAGTGT
gi|6273284|gb|AF191658.1|AF191      AAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGT
gi|6273287|gb|AF191661.1|AF191      AAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGT
gi|6273286|gb|AF191660.1|AF191      AAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGT
gi|6273290|gb|AF191664.1|AF191      AAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGT
gi|6273289|gb|AF191663.1|AF191      AAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTAT
gi|6273291|gb|AF191665.1|AF191      AAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGT
                                    ************************************ *********** *

gi|6273285|gb|AF191659.1|AF191      ACCAGA
gi|6273284|gb|AF191658.1|AF191      ACCAGA
gi|6273287|gb|AF191661.1|AF191      ACCAGA
gi|6273286|gb|AF191660.1|AF191      ACCAGA
gi|6273290|gb|AF191664.1|AF191      ACCAGA
gi|6273289|gb|AF191663.1|AF191      ACCAGA
gi|6273291|gb|AF191665.1|AF191      ACCAGA
                                    ******

generate the VCF

$ curl https://raw.github.com/biopython/biopython/master/Tests/Clustalw/opuntia.aln" |\
  java -jar dist/jvarkit.jar msa2vcf

##fileformat=VCFv4.1
##Biostar94573CmdLine=
##Biostar94573Version=ca765415946f3ed0827af0773128178bc6aa2f62
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth.">
##contig=<ID=chrUn,length=156>
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	gi|6273284|gb|AF191658.1|AF191	gi|6273285|gb|AF191659.1|AF191	gi|6273286|gb|AF191660.1|AF191	gi|6273287|gb|AF191661.1|AF191	gi|6273289|gb|AF191663.1|AF191	gi|6273290|gb|AF191664.1|AF191	gi|6273291|gb|AF191665.1|AF191
chrUn	8	.	T	A	.	.	DP=7	GT:DP	0:1	0:1	1:1	0:1	0:1	0:1	0:1
chrUn	13	.	A	G	.	.	DP=7	GT:DP	0:1	0:1	0:1	0:1	1:1	1:1	1:1
chrUn	56	.	ATATATATATA	ATA,A,ATATA	.	.	DP=7	GT:DP	1:1	2:1	2:1	2:1	3:1	3:1	0:1
chrUn	74	.	TCA	TAT	.	.	DP=7	GT:DP	0:1	0:1	1:1	0:1	0:1	0:1	0:1
chrUn	81	.	T	C	.	.	DP=7	GT:DP	0:1	0:1	0:1	0:1	1:1	1:1	1:1
chrUn	91	.	T	C	.	.	DP=7	GT:DP	1:1	1:1	0:1	0:1	0:1	0:1	0:1
chrUn	137	.	T	C	.	.	DP=7	GT:DP	0:1	1:1	0:1	0:1	0:1	0:1	0:1
chrUn	149	.	G	A	.	.	DP=7	GT:DP	0:1	0:1	0:1	0:1	1:1	0:1	0:1

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