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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?