Why Shouldn'T I Use Masking When Doing A Reference Alignment?

Question

[Joseph Hughes]

Hi all,

What are the problems that are associated with hard or soft-masking my reference before doing a reference alignment using a tool like BWA or Bowtie?

Answer 1

[Istvan Albert]

Two related questions with answers:

• Exome Sequencing: Masking The Non-Genic Sequences ?
• A: Which Aligners Recognize Soft-Masked Repeats In Reference Sequences?

[swbarnes2]

Second link appears to be broken...

[joeyfuerimmer]

Which Aligners Recognize Soft-Masked Repeats In Reference Sequences?