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Hi members
I recently tried to extract SNPs and InDels from a BAM file using Samtools/mpileup/bcftools and found that the SNPs and InDels are in concordance with what I view using Samtools TVIEW visualization. When I loaded the same BAM file on IGV or BAMview , I found a lot of changes in the alignments, and so the SNPs and InDels were not the same at many a locations. Someone, told me that IGV recalibrates the BAM file; this is not what I want. I have not checked Samscope or other visualization tools. Any recommendation for tools that would show the alignments of BAM as it is just as in TVIEW ?? The problem with TVIEW is that it is not much interactive and fancy.
Abi
I recently tried to extract SNPs and InDels from a BAM file using Samtools/mpileup/bcftools and found that the SNPs and InDels are in concordance with what I view using Samtools TVIEW visualization. When I loaded the same BAM file on IGV or BAMview , I found a lot of changes in the alignments, and so the SNPs and InDels were not the same at many a locations. Someone, told me that IGV recalibrates the BAM file; this is not what I want. I have not checked Samscope or other visualization tools. Any recommendation for tools that would show the alignments of BAM as it is just as in TVIEW ?? The problem with TVIEW is that it is not much interactive and fancy.
Abi