If you do not have an alignment file in the SAM format you may want to start with Introduction to mapping.
[samopen] SAM header is present: 1 sequences. |
[bam_sort_core] merging from 2 files... |
[mpileup] 1 samples in 1 input files <mpileup> Set max per-file depth to 8000 [bcfview] 100000 sites processed. [afs] 0:99910.349 1:52.764 2:36.886 [bcfview] 200000 sites processed. [afs] 0:99946.543 1:48.457 2:5.000 [bcfview] 300000 sites processed. [afs] 0:99976.591 1:5.410 2:17.999 [bcfview] 400000 sites processed. [afs] 0:99984.243 1:8.357 2:7.399 [bcfview] 500000 sites processed. [afs] 0:99970.803 1:23.197 2:6.000 [afs] 0:63952.773 1:6.227 2:2.000 |
Produces output.vcf from Bowtie and output.vcf from BWA.