To whom it may concern,
I want to work with SNP calling using GATK.
I`ve been trying to use the Picard`s AddOrReplaceReadGroups.jar tool to convert sam file to bam file.
But Picard stopped(without any error message). This size of sam file is 40Gb and I think this is bigger than my computer memory.
My file size is 30Gb fastq file.
My work flow is follow:
1) bwa index -a bwtsw hg19
2) bwa aln -t 6 hg19 sample.fastq > sample.sai
3) bwa samse hg19 sample.sai sample.fastq > sample.sam --> 40Gb
4) java -Djava.io.tmpdir=/tmp -Xmx8g -jar /myPath/AddOrReplaceReadGroups.jar \
INPUT=sample.sam OUTPUT=sample.addRG.bam \
SORT_ORDER=coordinate \
RGID=sample RGLB=sampleLIB RGPL=ILLUMINA \
RGPU=NONE RGSM=sample \
VALIDATION_STRINGENCY=LENIENT
---------------------------------------------------------------------------------------
Problem happens when I run step 4. Whenever I run this step, the process stop and I am not able to do anything.
I would appreciate any help.
I want to work with SNP calling using GATK.
I`ve been trying to use the Picard`s AddOrReplaceReadGroups.jar tool to convert sam file to bam file.
But Picard stopped(without any error message). This size of sam file is 40Gb and I think this is bigger than my computer memory.
My file size is 30Gb fastq file.
My work flow is follow:
1) bwa index -a bwtsw hg19
2) bwa aln -t 6 hg19 sample.fastq > sample.sai
3) bwa samse hg19 sample.sai sample.fastq > sample.sam --> 40Gb
4) java -Djava.io.tmpdir=/tmp -Xmx8g -jar /myPath/AddOrReplaceReadGroups.jar \
INPUT=sample.sam OUTPUT=sample.addRG.bam \
SORT_ORDER=coordinate \
RGID=sample RGLB=sampleLIB RGPL=ILLUMINA \
RGPU=NONE RGSM=sample \
VALIDATION_STRINGENCY=LENIENT
---------------------------------------------------------------------------------------
Problem happens when I run step 4. Whenever I run this step, the process stop and I am not able to do anything.
I would appreciate any help.
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