If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra

Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

From vcf to gvcf

manolismanolis Member ✭✭
edited December 2018 in Ask the GATK team


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 (./.).

Many thanks

Best Answer


Sign In or Register to comment.