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Old 03-25-2014, 09:30 PM   #1
alyamahmoud
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Location: Egypt, Saudi Arabia

Join Date: Nov 2013
Posts: 29
Default BWA-GATK pipeline showing weird results upon visulisation

Dear All

I am a novice to NGS. My intention is to discover SNPs between two strains (virulent versus avirulent) in malaria. I mapped illumina reads to reference genome using bwa aln and then bwa sampe, removed duplicates and then used Unified genotyper with hard filtering for SNPs calling.

The problem is that I get high percent of reads alignment at 10-20x coverage (at least 98% of the reads aligned properly according to samtools flagstat), however, when I try to visualise the results (bam/VCF view in artemis) most of the reads show mismatches !! Any clue ? Is this normal ?

Thank you very much
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Old 03-27-2014, 04:45 AM   #2
TiborNagy
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Yes, because BAM files does not mark mismatches, only indels. So samtools flagstat does not have any information about mismatches.
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