Heads up:
We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
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.
We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!

can I use indel realignment bam file for extract SNPs?

pat_patpat_pat Member
edited July 2017 in Ask the GATK team

Hi everybody,
I'm following the pipeline for VC in RNAseq and I have some doubts. At that moment I've done:
1)Split'N'Trim and reassign mapping qualities (output: split.bam)

2)Indel Realignment: at that point I create realignment targets ( java -jar ~/bin/GATK3.3/GenomeAnalysisTK.jar -T RealignerTargetCreator -R reference.fasta -I dedup.bam -o targetintervals.list) and indel realignment (java -jar ~/bin/GATK3.3/GenomeAnalysisTK.jar -T IndelRealigner -R ref -I dedup.bam -targetIntervals targetintervals.list -o realigned.bam)
output: realigned.bam

3)Variant calling:In this step I've run the command: java -jar GenomeAnalysisTK.jar -T HaplotypeCaller -R ref.fasta -I realigned.bam -dontUseSoftClippedBases -stand_call_conf 20.0 -o output.vcf, usind as input: realigned.bam
But I've run it only once, my first doubt is in this step, should I use a different command line to generate the output.vcf for INDELS and SNPs? or I can run it only one and filter later (as follow)?

4)Variant filtering:
Extract SNPs
java -jar ~/bin/GATK3.3/GenomeAnalysisTK.jar -T SelectVariants -R reference.fasta -V output.vcf -selectType SNP -o snps.vcf

Extract Indels
java -jar ~/bin/GATK/GenomeAnalysisTK.jar -T SelectVariants -R reference.fasta -V output.vcf -selectType INDEL -o indels.vcf

in both cases I use as vcf the output generated in variant calling, is that correct, or the vcf should be different?

Thank you very much in advance,


  • SheilaSheila Broad InstituteMember, Broadie admin


    I think you are asking if HaplotypeCaller generates both INDEL and SNP calls in the final VCF? If so, HaplotypeCaller does indeed produce both SNP and INDEL calls, so you do not need to run HaplotypeCaller twice.


Sign In or Register to comment.