dot-checkExRanges | Class to add ref/alt to GRanges |
filterReads | filter out reads based on mapq and LQ20 |
GAlnCheck | Check ref/alt counts for given GAlignments |
getReferenceSeq | Extract reference sequence |
MAP | MAP function for reduceByFile |
reAlign | Local re-align reads |
RefAltAln | Construct alternative reference sequence |
repReg | check repeat region |
verIndel | Verify Indel alignments |
viewAligns | viewAligns |
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