Need to convert a VCF into a gVCF so you can combine other data that wasn't generated by GATK? Well, this script is what you need.
Providing a VCF and a target BED file, this script will transform your plain single sample VCF into a GVCF (sort of). Rather than doing it correctly (which would be a more complicated process), this approach instead assumes that you have adequate coverage in your BED file. It will then add in your pre-specified values of GL, PL, GQ, and MIN_DP fields.
usage: main.py [-h] -v VCF -b BED -f FASTA [-o OUTNAME] [-M MIN_DEPTH] [-P PL]
[-V {DEBUG,INFO,WARNING,ERROR,CRITICAL}]
optional arguments:
-h, --help show this help message and exit
-v VCF, --vcf VCF VCF File to convert
-b BED, --bed BED Target BED file
-f FASTA, --fasta FASTA
Where is the reference genome (FASTA) file?
-o OUTNAME, --outname OUTNAME
What should the output file name be? [output.g.vcf]
-M MIN_DEPTH, --min_depth MIN_DEPTH
Dummy value for min_depth [20]
-P PL, --pl PL Dummy value for PL (Non zero genotypes) [99]
-V {DEBUG,INFO,WARNING,ERROR,CRITICAL}, --verbose {DEBUG,INFO,WARNING,ERROR,CRITICAL}
Set the logging level [INFO]
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