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.

Regarding Gatk output

I want to identify snps in my sequencing data.I am new in this field so i am just following guideline that you provided. i have paired end sequencing data (one sample) and according to documentation. i ran the programs and in the end i ran
java -Xmx32g -jar GenomeAnalysisTK.jar -T HaplotypeCaller -R genome.fasta -I realigned.bam -nct 14 -stand_call_conf 30 -o DK_new.vcf

After getting vcf file, i want to filter vcf file on the basis of allelic depth (DP) that describe in format column. Can you tell me how can i do this.

One more question about the DP value.. why DP value is different in info and format column???
i read the discussion about this and find that because of informative reads and uninformative reads. So it will always possible that allelic depth < total read depth at particular site. so it will better that to filter snps on basis of allelic depth than the total read depth.
I am totally confused that how can i filter snps ????

Please give suggestions about that.

Thanks & Regards


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