CONGA

(COpy Number variation Genotyping in Ancient genomes and low-coverage sequencing data)

CONGA is a genotyping algorithm for Copy Number Variations (large deletions and duplications) in ancient genomes. It is tailored for calling homozygous and heterozygous CNV genotypes at low depths of coverage using read-depth and read-pair information from a BAM file with Illumina short single-end reads.

Installation

Bioconda (recommended)

conda install -c bioconda conga

From source

Requirements

• htslib (included as submodule; http://htslib.org/)
• libbz2, liblzma, libcurl are required by htslib

Installing development libraries (requires sudo access): "sudo apt-get install zlib1g-dev libbz2-dev liblzma-dev libcurl4-openssl-dev"

Build and Run

git clone https://github.com/asylvz/CONGA --recursive
cd CONGA && make libs && make

./conga --input myinput.bam --ref human_g1k_v37.fasta \
	--dels known_dels.bed --dups known_dups.bed --out myoutput

Docker Usage

docker pull asylvz/conga
docker run --user=$UID -v /home/projects/conga:/input -v /home/projects/conga:/output asylvz/conga --input /input/myinput.bam --ref /input/human_g1k_v37.fasta --dels /input/known_dels.bed --dups /input/known_dups.bed --out /output/mydockertest

Output

CONGA produces three output files based on the --out prefix:

• <prefix>_svs.bed — Filtered SV calls (deletions and duplications combined), filtered by c-score and mappability.
• <prefix>_dels.bed — All deletion genotyping results with detailed metrics (observed/expected read depth).
• <prefix>_dups.bed — All duplication genotyping results with detailed metrics (observed/expected read depth).

Sample Genotype file (required)

You can use the "svcalls.sh" script under /scripts to generate CNV calls from the 1K Phase 3 SV call set

1	668630		850204
1	963826		974172
1	1171539		1179729
1	1249799		1265722
1	2374226		2379823
...

• The columns are "Chromosome Name" (TAB) "Start Position of a CNV" (TAB) "End Position of a CNV"
• Provide separate files for deletions (--dels) and duplications (--dups).

Mappability file (optional)

1	63913643	63913648	0.2
1	63913648	63913649	0.25
1	63913649	63913653	0.5
1	63913653	63913659	0.333333
...

Using a mappability file (--mappability) increases the accuracy of CONGA's predictions. We used the 100-mer mappability file from http://hgdownload.cse.ucsc.edu/goldenpath/hg19/encodeDCC/wgEncodeMapability/ and converted the bigWig file into a BED file using "bigWigToBedGraph".

• The columns are "Chromosome Name" (TAB) "Start" (TAB) "End" (TAB) "Mappability value"
  • Note that the mappability value should be between [0,1], where lower values indicate lower mappability intervals, i.e., repeat-rich regions, etc.

Repeats file (optional, only used with --rp)

You can optionally provide a repeats file to filter out reads in satellite regions using --reps. The file should be tab-delimited with 5 columns:

chr1	10000	20000	(CATTC)n	Satellite
chr1	50000	60000	L1ME1		LINE/L1

• The columns are "Chromosome Name" (TAB) "Start" (TAB) "End" (TAB) "Repeat Type" (TAB) "Repeat Class"
• This can be generated from RepeatMasker output. All repeats are loaded; satellite filtering (looking for "Satel" in type or class) is done at runtime.

Parameters

Required:

--input            Input file in sorted and indexed BAM format.
--out              Prefix for the output file names.
--ref              Reference genome in FASTA format.
--dels             Known deletion SVs in BED format.
--dups             Known duplication SVs in BED format.

Optional:

--mappability      Mappability file in BED format.
--reps             Repeat regions file to filter out satellite regions (only used with --rp).
--rp               Enable split-read and set read-pair support threshold for duplications (suggested for >5x).
--first-chr        Index of the first chromosome for genotyping (default: all).
--last-chr         Index of the last chromosome for genotyping (default: all).
--min-read-length  Minimum read length for read-pair analysis (default: 60).
--min-sv-size      Minimum CNV length (default: 1000).
--min-mapq         Minimum mapping quality threshold (default: no filter).
--c-score          Minimum c-score for filtering; lower is more conservative (default: 0.5).

Info:

--version          Print version and exit.
--help             Print help screen and exit.

Citation

Arda Söylev, Sevim Seda Çokoglu, Dilek Koptekin, Can Alkan, and Mehmet Somel. "CONGA: Copy number variation genotyping in ancient genomes and low-coverage sequencing data." PLOS Computational Biology 18, no. 12 (2022): e1010788. https://doi.org/10.1371/journal.pcbi.1010788