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Jeltje / varscan2

Scripts to run copynumber variation calls on tumor and normal BAM files using Varscan2
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mpileup crashes with large bam files #1

Closed jpfeil closed 7 years ago

jpfeil commented 7 years ago

[mpileup] 2 samples in 2 input files

Set max per-file depth to 4000 ERROR: Cannot finish /usr/local/bin/run_varscan because failed to find /data/tmp/varscan.5536/mpileup
Jeltje commented 7 years ago

We figured out this was due to mixing hg19 and GRCh37 inputs.