Hi All,
I try to do SNP calling using GATK. This is my first time to do such things and I generated the work flow as follows. Everything went well till I was blocked by RealignerTargetCreator. It seemed to cost 15 days per sample!
I don't know whether it was a normal speed with 300MB reference and 1GB bam file or not. Could anybody help me figure it out? I have 80 samples and obviously I don't have enough time to run this step.
Thanks for your time~!
My work flow (till RealignTargetCreator):
I used sga to do de novo assembly and I used the output file contigs.fa as reference.
bwa index -P contigs.fa -a bwtsw contigs.fa
bwa aln -t 4 contigs.fa R1.fq > R1.sai
bwa aln -t 4 contigs.fa R2.fq > R2.sai
bwa sampe contigs.fa R1.sai R2.sai R1.fq R2.fq > A.sam
samtools view -bST contigs.fa -o A_noRG.bam A.sam
java -Xmx20g -XX:PermSize=10g -XX:MaxPermSize=10g -jar /usr/share/picard/lib/AddOrReplaceReadGroups.jar INPUT=A_noRG.bam OUTPUT=A_std.bam SORT_ORDER=coordinate RGID=lib1_A RGLB=AA RGPL=illumina RGSM=lib1_A RGPU=none VALIDATION_STRINGENCY=LENIENT
java -Xmx20g -XX:PermSize=10g -XX:MaxPermSize=10g -jar /usr/share/picard/lib/MarkDuplicates.jar INPUT=A_std.bam OUTPUT=A_std_noduplicates.bam METRICS_FILE=A_std.duplicate_matrics REMOVE_DUPLICATES=true ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT
java -Xmx20g -XX:PermSize=10g -XX:MaxPermSize=10g -jar /usr/share/picard/lib/BuildBamIndex.jar INPUT=A_std_noduplicates.bam VALIDATION_STRINGENCY=LENIENT
java -Xmx20g -XX:PermSize=10g -XX:MaxPermSize=10g -jar /usr/share/GenomeAnalysisTK-2.1-10-gdbc86ec/GenomeAnalysisTK.jar -T RealignerTargetCreator -nt 8 -I A_std_noduplicates.bam -R contigs.fa -o A_forIndelAligner.intervals
I try to do SNP calling using GATK. This is my first time to do such things and I generated the work flow as follows. Everything went well till I was blocked by RealignerTargetCreator. It seemed to cost 15 days per sample!
![Confused](https://www.seqanswers.com/core/images/smilies/confused.png)
Thanks for your time~!
My work flow (till RealignTargetCreator):
I used sga to do de novo assembly and I used the output file contigs.fa as reference.
bwa index -P contigs.fa -a bwtsw contigs.fa
bwa aln -t 4 contigs.fa R1.fq > R1.sai
bwa aln -t 4 contigs.fa R2.fq > R2.sai
bwa sampe contigs.fa R1.sai R2.sai R1.fq R2.fq > A.sam
samtools view -bST contigs.fa -o A_noRG.bam A.sam
java -Xmx20g -XX:PermSize=10g -XX:MaxPermSize=10g -jar /usr/share/picard/lib/AddOrReplaceReadGroups.jar INPUT=A_noRG.bam OUTPUT=A_std.bam SORT_ORDER=coordinate RGID=lib1_A RGLB=AA RGPL=illumina RGSM=lib1_A RGPU=none VALIDATION_STRINGENCY=LENIENT
java -Xmx20g -XX:PermSize=10g -XX:MaxPermSize=10g -jar /usr/share/picard/lib/MarkDuplicates.jar INPUT=A_std.bam OUTPUT=A_std_noduplicates.bam METRICS_FILE=A_std.duplicate_matrics REMOVE_DUPLICATES=true ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT
java -Xmx20g -XX:PermSize=10g -XX:MaxPermSize=10g -jar /usr/share/picard/lib/BuildBamIndex.jar INPUT=A_std_noduplicates.bam VALIDATION_STRINGENCY=LENIENT
java -Xmx20g -XX:PermSize=10g -XX:MaxPermSize=10g -jar /usr/share/GenomeAnalysisTK-2.1-10-gdbc86ec/GenomeAnalysisTK.jar -T RealignerTargetCreator -nt 8 -I A_std_noduplicates.bam -R contigs.fa -o A_forIndelAligner.intervals
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