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I am calling indel in pooled samples using this command:
java -jar -Xmx2g /PATH/2.1.13/GenomeAnalysisTK.jar -l INFO -T UnifiedGenotyper -I pool1.bam -I pool2.bam --out INDEL.vcf -R /reference.fa -glm INDEL
Currently i donot have any information of already known indels.
1.Do i need to first realign (RealignerTargetCreator and IndelRealigner) and then call indels even for pooled data?
2. How different will this be for calling indel on individual sample?
Looking forward for your suggesions.
with thanks sasha