## Overview

At this point, you should have a BAM file of barcoded alignments. This next step is a series of filters to remove reads that do not match certain criteria.

### Repeat masking

We use bedtools to discard reads that overlap the annotations in a mask file. The mask file is actually a composite of two separate mask files:

* UCSC repeatmasker, millidiv less than 140
* mm10 or hg38 blacklisted regions v2 

The composite mm10 and hg38 mask file that we use can be found in the main directory of the SPRITE-DNA pipeline.

```
bedtools intersect -v -a example.DNA.chr.bam -b mask_file.bed >
example.DNA.chr.masked.bam
```