invs_remap's Introduction

invs_remap

A repo collecting scripts and information for our read remapping procedure for better detection of inversions ~50bp - 1kbp

Approach

First step

Calculate the coverage AND the 'matchrate' in 50bp bins

Second Step

Select the regions that have a high mismatch rate and for which mismatched bps cover at least 10% of the total mismatches.

Third Step

Remove the overlapping SD and centromeric regions

Fourth Step

Remap these regions with NGMLR

Fifth Step

Call SVs on the remapped regions with Delly

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