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

Hello,
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

Answers

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