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
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
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