Samtools

Setup output directory.

If you do not have a alignment file in the SAM format you may want to start with Introduction to mapping.

Prepare reference file.

Prepare alignment file.

Convert SAM to BAM format.

[samopen] SAM header is present: 1 sequences.

Variant call output.

[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
[bam_pileup_core] the input is not sorted (reads out of order)
[afs] 0:0.000 1:0.000 2:0.000
[bam_plp_destroy] memory leak: 1. Continue anyway.