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Code Block
languagebash
titletype (or copy) these 3 commands, waiting for the idev session to open after the first.
idev -A UT-2015-05-18
cp $BI/gva_course/snv_tutorial_fix/full_snv_pipeline .
./full_snv_pipeline
Code Block
languagebash
titleThis is the output you will see
[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] 0:99968.324 1:23.090 2:8.586
[bcfview] 200000 sites processed.
[afs] 0:99972.734 1:22.265 2:5.001
[bcfview] 300000 sites processed.
[afs] 0:99969.505 1:25.152 2:5.343
[bcfview] 400000 sites processed.
[afs] 0:99977.665 1:19.328 2:3.007
[bcfview] 500000 sites processed.
[afs] 0:99964.202 1:24.792 2:11.006
[bcfview] 600000 sites processed.
[afs] 0:99979.628 1:9.529 2:10.843
[afs] 0:49405.456 1:8.543 2:1.001

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