Notice:
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.
Attention:
We will be out of the office on October 14, 2019, due to the U.S. holiday. We will return to monitoring the forum on October 15.

Ensembl GRCh38 indels and dsnp vcf files

samuelriverosamuelrivero Washington DCMember
edited May 2018 in Ask the GATK team

Hello,

I am using GATK3.8 to call variants in RNA-seq data. I am following the best practices for RNA-seq (https://software.broadinstitute.org/gatk/documentation/article.php?id=3891). My problem is during the indel realignment and base calibration steps. I have used the Ensembl GRCh38 genome version to map the reads. The indels and dsnp vcf files I can download from the resource bundle (hg38) have different chromosome notation and contig names (In my bam file chromosomes contain just number, ie "1", and in the vcf the format is "chr1"). Is there any indels and dsnp vcf files with the chromosome notation for Ensembl ? I can change the chromosome format in the vcf files but I dont know if this can be a problem in the next steps of the workflow.

Thanks

Sam

Post edited by samuelrivero on

Best Answer

Answers

  • samuelriverosamuelrivero Washington DCMember

    I have downloaded them from Ensembl , but I am having issues because in some lines the ALT field is empty. I will remap my samples using your hg38 reference.

    Thanks

Sign In or Register to comment.