[WGS] how to correctly visualize long indels (50nt+)
Hi All, I was wondering if there is any tool that can correctly visualize long indels (eg known deletions that are 50bp+ long). Bam files were aligned with BWA and vcf calls were done with GATK 3.x I tried to use samtools to extract the range of reads from the final bam (+/- 1000bp) but IGV (2.8.13) does not seem to show the expected junctions. thanks,
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memento1984_1 •
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could be that abra and indel realignment will help