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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 (./.).