SV Re-genotyping Methods for 10X Genomics

Installing

Download the source code:

git clone https://github.com/tobiasrausch/tenX.git

cd tenX/

Add the dependencies (Htslib, Boost, and Delly):

git submodule init

git submodule update

Add the Boost sub-libraries:

cd src/modular-boost

git submodule init

git submodule update

Build the programs:

cd ../../

make all

Example

Download the NA12878 10X Genomics phased bam file from http://10xgenomics.com/ and the 1000 Genomes structural variant (SV) release from the EBI ftp site:

wget 'ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/integrated_sv_map/ALL.wgs.integrated_sv_map_v2.20130502.svs.genotypes.vcf.gz'

Run the haplotype-aware SV re-genotyping of the SV site list:

./genoDEL -v ALL.wgs.integrated_sv_map_v2.20130502.svs.genotypes.vcf.gz NA12878.10X.bam > del.tsv

Compare 1000 Genomes phased & imputed genotypes with 10X Genomics derived genotypes:

python compareGeno.py -t del.tsv

Estimate phasing accuracy:

python comparePhasing.py -t del.tsv