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Use Freebayes parameters in use for 1000 genomes calling

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chapmanb committed May 16, 2012
1 parent 0ab42fd commit 680ebb3694765e945f0008471aea39edfb0136d7
Showing with 1 addition and 1 deletion.
  1. +1 −1 bcbio/variation/freebayes.py
@@ -37,7 +37,7 @@ def run_freebayes(align_bam, ref_file, config, dbsnp=None, region=None,
with file_transaction(out_file) as tx_out_file:
cl = [config["program"].get("freebayes", "freebayes"),
"-b", align_bam, "-v", tx_out_file, "-f", ref_file,
"--left-align-indels"]
"--left-align-indels", " --no-filters", "--use-mapping-quality"]
cl += _freebayes_options_from_config(config["algorithm"], out_file, region)
subprocess.check_call(cl)
return out_file

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