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can I use indel realignment bam file for extract SNPs?
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)
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)?
java -jar ~/bin/GATK3.3/GenomeAnalysisTK.jar -T SelectVariants -R reference.fasta -V output.vcf -selectType SNP -o snps.vcf
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,