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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, Moderator 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.


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