GATK IndelRealigner returns empty output file

[bjfan]

Hello everyone,

I am for the first time to perform an analysis of exome sequencing data (paired-end). After having aligned the sequence data to the reference genome by BWA and sorted and indexed the .bam file by samtools, I am applying GATK (v1.0.3423) to local realignment. The step #1 (to identify target regions for realignment) works OK. However, the step #2 (to realign .bam to get better Indel calling) returns an empty output file (0 bytes).

Here are the commands that I used:

# step 1: Identify target regions for realignment

java -jar /opt/GenomeAnalysisTK/GenomeAnalysisTK.jar -T RealignerTargetCreator -R /home/bf13/RefSeq/human_g1k_v37.fasta -I aln.sorted.bam -o aln.intervals

# step 2: Realign .bam to get better Indel calling

java -jar /opt/GenomeAnalysisTK/GenomeAnalysisTK.jar -T IndelRealigner -R /home/bf13/RefSeq/human_g1k_v37.fasta -I aln.sorted.bam -targetIntervals aln.intervals -o aln.sorted.realigned.bam

Here are the job report for # step 2 (I submitted this job to LSF):

------------------------------------------------------------
Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
# step 7: Realign BAM to get better Indel calling

java -jar /opt/GenomeAnalysisTK/GenomeAnalysisTK.jar -T IndelRealigner -R /home/bf13/RefSeq/human_g1k_v37.fasta -I aln.sorted.bam -targetIntervals aln.intervals -o aln.sorted.realigned.bam

------------------------------------------------------------

Successfully completed.

Resource usage summary:

CPU time : 8954.74 sec.
Max Memory : 2043 MB
Max Swap : 12557 MB

Max Processes : 4
Max Threads : 32

The output (if any) follows:
-------------------------------------------------------------

Could anyone give some advices?

Thanks,
Baojian

[wjeck]

I seem to be seeing the same or a similar problem. GATK runs, or for all appearances runs, exits 'successfully' and then creates an empty .bam file . I've tried a couple of things with no luck...

[bjfan]

I have this problem solved by installation of the latest version of GATK (v1.0.5777). I guess the reason is that older versions of GATK use "--output <filename>" other than "-o <filename>" for this specific IndelRealigner.

[wjeck]

Wow, well I will go try that out! Many thanks.