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Once I run ABRA, I always get the following error. Would you please look into it? Thanks.
Loading native library from: /scratch/BREIGR0124_VAxg_01_1408120760/libAbra.so
Loading reference map: /site/n…
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The indel realigner is a large hunk of code. It "works" right now, but we need to go through and fully debug the performance and accuracy of the feature.
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Currently, indel realignment uses a mismatch quality score based approach for generating alternate consensuses. It is desirable to also support Smith-Waterman for generating consensuses. We have a Smi…
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@Garyfallidis and @alexis-roche - it seems that moving the transformations(e.g., syn) from dipy to nireg would now make some sense.
satra updated
9 years ago
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## I am getting the following error with abra v0.77:
Thu Jun 12 19:48:43 CEST 2014 : Aligning contigs
Running: [bwa mem -t 5 /data/broad/human_g1k_v37.fasta abra_temp_dir/all_contigs.fasta > abra_tem…
Gig77 updated
10 years ago
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My colleague Paolo Uva noticed that the gatk2_unified_genotyper tool creates a number of threads which is 6 times the number of cores it has been assigned in job_conf.xml (i.e. $GALAXY_SLOTS). This is…