I have a few BAM files from collaborators and I do not know if these were indel-realigned. People who was working on these files are no longer working in the lab, so I have no sources of information about details of these alignments. Is there a way to check if these files were indel-realigned?
search a program group in the bam header for gatk IndelRealigner
@PG ID:bam_realignment_around_known_indels.1 PN:GenomeAnalysisTK PP:gatk_target_interval_creator.1 VN:1.2-29-g0acaf2d CL:java $jvm_args -jar GenomeAnalysisTK.jar -T IndelRealigner -R $reference_fasta -I $bam_file -o $realigned_bam_file -targetIntervals $intervals_file -known $known_indels_file(s) -LOD 0.4 -model KNOWNS_ONLY -compress 0 --disable_bam_indexing
@PG ID:bam_realignment_around_known_indels.2 PN:GenomeAnalysisTK PP:gatk_target_interval_creator.2 VN:1.2-29-g0acaf2d CL:java $jvm_args -jar GenomeAnalysisTK.jar -T IndelRealigner -R $reference_fasta -I $bam_file -o $realigned_bam_file -targetIntervals $intervals_file -known $known_indels_file(s) -LOD 0.4 -model KNOWNS_ONLY -compress 0 --disable_bam_indexing
@PG ID:bam_realignment_around_known_indels.3 PN:GenomeAnalysisTK PP:gatk_target_interval_creator.3 VN:1.2-29-g0acaf2d CL:java $jvm_args -jar GenomeAnalysisTK.jar -T IndelRealigner -R $reference_fasta -I $bam_file -o $realigned_bam_file -targetIntervals $intervals_file -known $known_indels_file(s) -LOD 0.4 -model KNOWNS_ONLY -compress 0 --disable_bam_indexing