README.md

VCFresolve

VCFresolve aims to sequence resolve the VCF files...

Downloading VCFresolve

git clone https://github.com/asylvz/VCFresolve.git

Quick Start (To resolve the sequences of the SVs)

python vcf-resolve --resolve -g Reference_Genome -v VCF -a Repeat_Annotation -o Output

Optionally you can sequence resolve only the precise calls, i.e., the calls that don't have IMPRECISE keyword

python vcf-resolve --resolve -g Reference_Genome -v VCF -a Repeat_Annotation -o Output --precise

Running Mendelian Filter for trios

python vcf-resolve --mendelian -v VCF -o Output

Downloading the repeat annotation file

Using UCSC sequence and annotations download page;

For repeat annotations, navigate to the related genome's "Full data set" page and download the RepeatMasker .out files (i.e., http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/chromOut.tar.gz is for human genome GRCh37/hg19)

Extract the files into a folder and merge them into a single .out file:

cat * >reps.out

*Alternatively, if the files are inside directories for each chromosome, then use:

cat */* >reps.out

Downloading the reference genome file

Using UCSC sequence and annotations download page;

For reference genome, navigate to the related genome's "Full data set" page and download the FASTA files (i.e., http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/chromFa.tar.gz is for human genome GRCh37/hg19)

Extract the files into a folder and merge them into a single .fasta file:

cat * >ref.fasta