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Hi Brad,
I am trying to use bcbio-nextgen to analysis whole-exome seq data. However, an error stopped the process, the detailed info is:
[2014-09-02 22:42] Finalizing variant calls: C3, freebayes
[2…
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touch test.bed
latest version:
samtools mpileup -DV -C50 -pm3 -F0.2 -d 10000 -ug test.bed > out.1
[mpileup] 1 samples in 1 input files
[W::sam_read1] parse error at line 1
Successfully completes.
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I'm running Gemini on two systems (personal Mac which I updated to 0.6 and cluster which hasn't been updated yet). The unit tests all passed when I updated my Mac.
However I have a database I gene…