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bcbio / bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
https://bcbio-nextgen.readthedocs.io
MIT License
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sv using bam files #682

Closed kspham closed 9 years ago

kspham commented 9 years ago

I used bam input (given by bcbio when running variantcalling pipeline) for sv, but somehow the lumpy refused to run:( is there anyway to bypass this?

a 167 168 def run(items): 169 """Perform detection of structural variations with lumpy, using bwa-mem alignment. 170 """ 171 if not all(utils.get_in(data, ("config", "algorithm", "aligner")) == "bwa" for data in items): --> 172 raise ValueError("Require bwa-mem alignment input for lumpy structural variation detection") 173 work_dir = utils.safe_makedir(os.path.join(items[0]["dirs"]["work"], "structural", items[0]["name"][-1], 174 "lumpy")) 175 full_bams, sr_bams, disc_bams = [], [], [] 176 for data in items:

ValueError: Require bwa-mem alignment input for lumpy structural variation detection

chapmanb commented 9 years ago

Son; Thanks for the heads up. Pall had also brought up this issue earlier (#662). I relaxed the verification so now it won't try to verify it if you don't specify an aligner. It's a pretty crude sanity-check so was only meant to give people a heads up. If you update to the latest development version it should hopefully work for you without any issues. Thanks again.