We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
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.
What's doing the MarkDuplicates?
i have a ION PGM sequencing, i follow the best practices to do the variant calling
my command line:
bwa mem -M -R '@RG\tID:group1\tSM:sample1\tPL:IONTORRENT\tLB:lib1\tPU:unit1' /home/horus/Escritorio/PGM/primirna/references/hg19usar.fa 1.fq.gz > 1_aligned_reads.sam
java -jar /home/horus/Instaladores/picard-tools-1.110/picard-tools-1.110/SortSam.jar INPUT=1_aligned_reads.sam OUTPUT=1_sorted_reads.bam SORT_ORDER=coordinate
java -jar /home/horus/Instaladores/picard-tools-1.110/picard-tools-1.110/MarkDuplicates.jar INPUT=1_sorted_reads.bam OUTPUT=1_dedup_reads.bam METRICS_FILE=1_metrics.txt
java -jar /home/horus/Instaladores/picard-tools-1.110/picard-tools-1.110/BuildBamIndex.jar INPUT=1_dedup_reads.bam
java -jar /home/horus/Instaladores/GenomeAnalysisTK-3.1-1/GenomeAnalysisTK.jar -T RealignerTargetCreator -R /home/horus/Escritorio/PGM/primirna/references/hg19usar.fa -I 1_dedup_reads.bam -known /home/horus/Escritorio/PGM/primirna/references/Mills_and_1000G_gold_standard.indels.b37.vcf_nuevo -o 1_target_intervals.list
java -jar /home/horus/Instaladores/GenomeAnalysisTK-3.1-1/GenomeAnalysisTK.jar -T IndelRealigner -R /home/horus/Escritorio/PGM/primirna/references/hg19usar.fa -I 1_dedup_reads.bam -targetIntervals 1_target_intervals.list -known /home/horus/Escritorio/PGM/primirna/references/Mills_and_1000G_gold_standard.indels.b37.vcf_nuevo -o 1_realigned_reads.bam
after the IndelRealigner step, i check the sorted_reads.bam and the bam i get with the IndelRealigner on IGV...
in the position that show the image, after the realignment only 5 reads are keep, the question is why all the reads that have the variant in the reverse strand are gone?
i don't understend, these reads are placed somewhere else in the alignment?