Gatk - Identify Regions To Realign
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Find places on genomes with indels for realignment.

**Location**

- *Filepath:* <SnakeLines_dir>/rules/mapping/postprocess/realigned/gatk.snake
- *Rule name:* gatk__identify_regions_to_realign

**Input(s):**

- *ref:* Reference genomic sequences in FASTA format
- *fai:* Reference index for faster sequence retrieval
- *dict:* Reference index for faster sequence retrieval
- *bam:* Mapped reads for realignment in BAM format
- *bam:* Mapped reads index for faster alignment retrieval

**Output(s):**

- *intervals:* Regions that need to be realigned

Gatk - Realign Regions
--------------------------

Realign regions locally in places with indels that are problematic for standard mappers.

**Location**

- *Filepath:* <SnakeLines_dir>/rules/mapping/postprocess/realigned/gatk.snake
- *Rule name:* gatk__realign_regions

**Input(s):**

- *ref:* Reference genomic sequences in FASTA format
- *bam:* Mapped reads for realignment in BAM format
- *intervals:* Regions that need to be realigned

**Output(s):**

- *bam:* Realigned reads in BAM format

