The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.
From vcf to gvcf
I read this question and I opened a new thread to avoid confusion.
I know that you do not support single-end data analysis. I have many deduplicated BAM files and their vcf, without the possibility to go back with the same software to create g.vcf files. Is there any gatk tool to help me to create g.vcf files starting from BAM and VCF? I need to merge these g.vcf files for downstream analysis.
For example, to use as -L the variants position and then to use the BAM files to extract the number of reads of the reference in the samples that do not have those variants. That just to know if a ref. position is covered (0/0) or uncovered (./.).