Samtools - Convert Sam To Bam

Convert .bam to .sam.

Location

• Filepath: <SnakeLines_dir>/rules/shared/mapping/index/samtools.snake
• Rule name: samtools__convert_sam_to_bam

Input(s):

• bam: Mapped reads in bam format

Output(s):

• sam: Mapped reads in sam format

Samtools - Bam Index

Generate .bai index to .bam files to quick recover reads from genomic location of interest.

Location

• Filepath: <SnakeLines_dir>/rules/shared/mapping/index/samtools.snake
• Rule name: samtools__bam_index

Input(s):

• bam: Mapped reads in bam format

Output(s):

• bai: Index to mapped reads for enable fast read retrieval from desired genomic region