What's doing the MarkDuplicates?
Posted in Ask the GATK team | Last updated on 2014-03-28 16:15:25


Comments (6)

Hello,

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?


Return to top Comment on this article in the forum