Indel realigner introducing errors
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Hi

I'm indel realigning with version 2.4-9 using generic commands such as:

java -Xmx4g -jar /path/to/GenomeAnalysisTK.jar \ -T RealignerTargetCreator \ -R /path/to/reference.fasta \ -I /path/to/input.bam \ -o /path/to/realigner.intervals

java -Xmx4g -jar /path/to/GenomeAnalysisTK.jar \ -T IndelRealigner \ -R /path/to/reference.fasta \ -I /path/to/sample-level.bam \ -targetIntervals /path/to/realigner.intervals.from.rtc \ -o /path/to/realigned.bam \ -model USE_SW \ -LOD 0.4

In most cases this is working fine, but in a few cases it is introducing artefacts that subsequently cause the bam file to fail Picard's ValidateSamFile, and in a couple of cases it introduces errors that can't be fixed by CleanSam and/or FixMateInformation.

Here's an example of an error that can be fixed by CleanSam:

Before indel realignment:

HS24_08564:7:2311:4630:19372#87 69 AAKM01002546 471 0 * = 471 0 HS24_08564:7:2311:4630:19372#87 137 AAKM01002546 471 25 100M = 471 0

After indel realignment:

HS24_08564:7:2311:4630:19372#87 69 AAKM01002546 471 0 * = 471 0 HS24_08564:7:2311:4630:19372#87 137 AAKM01002546 471 35 91M1D9M = 471 0

Here's an example of an error that can't be fixed:

Before indel realignment:

HS24_10061:6:1312:10172:98346#54 69 AAKM01002280 649 0 * = 649 0 HS24_10061:6:1312:10172:98346#54 137 AAKM01002280 649 37 100M = 649 0

After indel realignment:

HS24_10061:6:1312:10172:98346#54 69 AAKM01002280 649 0 * = 649 0 HS24_10061:6:1312:10172:98346#54 137 AAKM01002280 649 47 91M2D9M0S = 649 0

Is this a known bug? Any chance of a fix?

Thanks!

Richard


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