Samtools

Setup output directory.

If you do not have an 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.

Sort BAM file.

[bam_sort_core] merging from 2 files...

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.