Question: How to check if BAM is indel-realigned?
0
gravatar for Alice
11 months ago by
Alice270
USA
Alice270 wrote:

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?

ADD COMMENTlink modified 11 months ago • written 11 months ago by Alice270
2
gravatar for Pierre Lindenbaum
11 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum118k wrote:

search a program group in the bam header for gatk IndelRealigner

e.g:https://github.com/samtools/samtools/blob/9df632114a537f57928e4b2c17fbb1928679f877/test/dat/mpileup.1.sam

@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
ADD COMMENTlink written 11 months ago by Pierre Lindenbaum118k

yay it worked! thanks

ADD REPLYlink written 11 months ago by Alice270
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