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c_ro87 11-30-2015 10:59 AM

Illumina Truseq Pair end
Hello, I have data from a custom truseq design.

The reads alignment was done using BWA, and variant calling using GATK following the best practices.

From the image, the bottom panel shows the alignment for the data after realignment around indels and score recalibration, you can see a peak in the midlle where coverage is the double than in both sides. This is the portion where the pairs overlapp, my first question is, if this is a normal behaviour, or maybe i'm too restrict when do my adapters removal?
This is the command line i use:
../../../../bin/fastq-mcf -o SAR093-2015/SAR093-2015-01-00001_S2_L001_R1_001_adap.fastq -o SAR093-2015/SAR093-2015-01-00001_S2_L001_R2_001_adap.fastq -l 50 -q 20 -x 10 -u -P 33 ../../../../data/adaptadores_truseq/adaptadores.txt SAR093-2015/SAR093-2015-01-00001_S2_L001_R1_001.fastq SAR093-2015/SAR093-2015-01-00001_S2_L001_R2_001.fastq &>r.log

The upper panel is the bamout generated after the GATK variant calling, and this show that the left part of the reads now is missing, any comments on this?

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