gravatar for memento1984_1

2 hours ago by

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.

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