If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
I'm using IndelRealigner, and it seems to take long time, from 5 to 8h, I have a strange sensation that I may not put the right commands but I'm not sure. Previously of what I show below I have Marked duplicates with MarkDuplicates.
/home/Programas/samtools-0.1.19/samtools index /local/ktroule/SNPiR/Panc047/accepted_hits_RG_Reordered_deduplicated.bam java -Xmx20g -jar /home/Programas/GATK-3.1-1-g07a4bf8/GenomeAnalysisTK.jar -T RealignerTargetCreator -R /local/Referencias/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.fa -I /local/SNPiR/Panc042/accepted_hits_RG_Reordered_deduplicated.bam --unsafe ALLOW_N_CIGAR_READS --known /local/Referencias/HG19/Mills_and_1000G_gold_standard.indels.hg19.vcf -o /local/SNPiR/Panc042/Panc042_indel.intervals java -Xmx20g -jar /home/Programas/GATK-3.1-1-g07a4bf8/GenomeAnalysisTK.jar -T IndelRealigner --targetIntervals /local/SNPiR/Panc042/Panc042_indel.intervals -R /local/Referencias/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.fa --unsafe ALLOW_N_CIGAR_READS -I /local/SNPiR/Panc042/accepted_hits_RG_Reordered_deduplicated.bam -o /local/SNPiR/Panc042/accepted_hits_RG_Reordered_deduplicated_Realigned.bam
This is not really about an error, but about If the program takes that long and about if the parameters I have used are the rights ones, as I have seen that few ones use the downsampling.
Finally, if I have not read wrongly InderRealigner does not support multithread, at least not directly from the program.
thanks for yor time.