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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
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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