MEIGA-PAV

MEIGA-PAV is a computational method for the annotation of mobile element insertions (MEI) in a VCF containing sequence-resolved structural variation (SV) calls. Although it has been designed to process SVs derived from the Phased Assembly Variant Caller (PAV; https://github.com/EichlerLab/pav), it should be compatible with the output of any long-read variant callers, as long as the sequence for insertion events is included in the VCF.

MEIGA-PAV was developed for the Human Genome Structural Variation Consortium (HGSVC)

Ebert et al., “Haplotype-Resolved Diverse Human Genomes and Integrated Analysis of Structural Variation,” Science, February 25, 2021, eabf7117, https://doi.org/10.1126/science.abf7117.

Download

Two different ways:

• Go to the releases tab and download the latest release.

• Clone the git repository in case you want the latest version of the code:

# Move into the folder in which you want to clone the repositoy.
$ cd ~/apps
# Clone it.
$ git clone https://github.com/Chimera-tools/ChimPipe.git

MEIGA-PAV does not require any further installation step. It is written in Python and can be run as a standalone application on diverse Linux systems.

Requirements

1. Hardware:

   • 64-bits CPU

2. Software:

   • 64-bit Linux System
   • Python v3.6 or higher
   • paftools v.r755 (https://github.com/lh3/minimap2/tree/master/misc)
   • bwa-mem v0.7.17 (https://github.com/lh3/bwa)
   • minimap2 v2.1 (https://github.com/lh3/minimap2)

3. Python libraries

   • pysam
   • cigar
   • numpy
   • itertools
   • Biopython

Input

MEIGA-PAV takes as input 6 mandatory arguments:

1. VCF: Input VCF file containing sequence-resolved structural variation calls.
2. consensus: Fasta file containing consensus sequences for retrotransposon subfamilies (Alu, L1 and SVA).
3. reference: Fasta file for the human genome reference. Use same chromosome labeling nomenclature as for the input VCF. BWA-mem index need to be located in the same folder
4. mt_reference: Fasta file for the mitochrondrial genome reference.
5. sampleID: Output VCF file will be named accordingly.
6. outDir: Output directory.

Execution

python MEIGA-PAV.py freeze3.sv.alt.vcf consensusDb.fa GCA_000001405.15_GRCh38_no_alt_analysis_set_no_chr_MT.fna chrM.fa 'PAV_MEI_MEIGA.freeze3' -o freeze3

File availability:

• Example VCF file for testing purposes can be downloaded from the 1000 genomes data portal (http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/HGSVC2/release/v1.0/integrated_callset/)
• The database of consensus retrotransposon sequences is provided in the /execution folder.
• Reference genome sequences can be downloaded from the UCSC browser (ftp://hgdownload.soe.ucsc.edu/goldenPath).

Output

MEIGA-PAV produces as output a standard VCF file containing the subset of insertions from the input VCF corresponding to MEI. MEI annotation information is included in the following additional INFO fields:

* ITYPE: Type of insertion. Solo retrotransposon insertion, partnered or orphan transduction. 
* FAM: Repeat family (Alu, L1 or SVA)
* 3PRIME: Flag indicating a 3-prime partnered transduction
* 5PRIME: Flag indicating a 5-prime partnered transduction
* CYTOID: Source element cytoband identifier (for transductions)   
* RETRO_LEN: Length for the inserted retrotransposon
* TRUNCATION_5_LEN: Length for 5-prime truncation 
* TRUNCATION_3_LEN: Length for 3-prime truncation
* INVERSION_LEN: Length for 5-prime inversion
* RETRO_COORD: Coordinates with respect to the consensus L1 for the retrotransposon insertion
* IS_FULL: Flag indicating a full length mobile element insertion  
* ORF1: Flag indicating the existance of a funtional ORF1 for L1s
* ORF2: Flag indicating the existance of a funtional ORF2 for L1s  
* COMPETENT: Flag indicating that the insertion is a potential competent full-length L1 with intact ORFs    
* TDCOORD_5PRIME: Genomic coordinates for 5-prime transduction
* TDCOORD_3PRIME: Genomic coordinates for 3-prime transduction
* TDLEN_5PRIME: Length of 5-prime transduction 
* TDLEN_3PRIME: Length of 3-prime transduction 
* STRAND: Insertion DNA strand (+ or -)

An example of VCF output (PAV_MEI_MEIGA.freeze3.vcf) is provided in the /execution folder. This results from the annotation of the input VCF (freeze3.sv.alt.vcf) included in the folder as well as an example

License

MEIGA-PAV is distributed under GPL-3.0 License

Cite MEIGA-PAV

Ebert et al., “Haplotype-Resolved Diverse Human Genomes and Integrated Analysis of Structural Variation,” Science, February 25, 2021, eabf7117, https://doi.org/10.1126/science.abf7117 (PMID: 33632895).

Contact

Please open a case on the Github page for problems.

You may also contact Bernardo Rodriguez-Martin directly (e-mail omitted to reduce SPAM). MEIGA-PAV was developed in the lab of Dr. José Tubio at CiMUS and Dr. Jan Korbel at EMBL.