Hello,
I'm attempting to use GATK 2.3-9-ge5ebf34 to re-align some RNA-seq datasets. Below is the code I'm using.
java -Xms16g -jar ~/bin/GenomeAnalysisTK-2.3-9-ge5ebf34/GenomeAnalysisTK.jar -T IndelRealigner -R ../../../transcripts/reference_wMT.fa -I fat_no_dup.bam -targetIntervals fat_no_dup.intervals -o fat_nd_realigned.bam
I'm receiving 2 errors that occur at many locations in the output. The first is below:
IndelRealigner - When first element of the alt consensus is M, the second one must be I or D. Actual: 85M208M2D15M.
I see that the issue is there are 2 M fields when it is only expecting 1. But I'm unsure of what this means, or what I can do to fix it. The bam file was aligned using tophat and allowing only 1 alignment per read. Any thoughts?
The second error is:
IndelRealigner - Not attempting realignment in interval 12:26475533-26475760 because there are too many reads.
I know the issue here is there are too many reads at that interval, so I have to increase the -maxReadsForRealignment setting. Does anyone know of a way to determine what the highest coverage is for one of these regions, so I can set the max reads above that level, instead of picking a random number and trying again? Thanks!
I'm attempting to use GATK 2.3-9-ge5ebf34 to re-align some RNA-seq datasets. Below is the code I'm using.
java -Xms16g -jar ~/bin/GenomeAnalysisTK-2.3-9-ge5ebf34/GenomeAnalysisTK.jar -T IndelRealigner -R ../../../transcripts/reference_wMT.fa -I fat_no_dup.bam -targetIntervals fat_no_dup.intervals -o fat_nd_realigned.bam
I'm receiving 2 errors that occur at many locations in the output. The first is below:
IndelRealigner - When first element of the alt consensus is M, the second one must be I or D. Actual: 85M208M2D15M.
I see that the issue is there are 2 M fields when it is only expecting 1. But I'm unsure of what this means, or what I can do to fix it. The bam file was aligned using tophat and allowing only 1 alignment per read. Any thoughts?
The second error is:
IndelRealigner - Not attempting realignment in interval 12:26475533-26475760 because there are too many reads.
I know the issue here is there are too many reads at that interval, so I have to increase the -maxReadsForRealignment setting. Does anyone know of a way to determine what the highest coverage is for one of these regions, so I can set the max reads above that level, instead of picking a random number and trying again? Thanks!
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