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Old 03-25-2014, 09:30 PM   #1
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
alyamahmoud is offline   Reply With Quote
Old 03-27-2014, 04:45 AM   #2
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Location: Budapest

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Posts: 329

Yes, because BAM files does not mark mismatches, only indels. So samtools flagstat does not have any information about mismatches.
TiborNagy is offline   Reply With Quote

artemis, bwa, gatk, snps, vcf

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