marchoeppner

Script join_aug_pred.pl incompatible with option --uniqueGeneId

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As the title states, the script for joining Augustus predictions across split jobs does not work if the option "--uniqueGeneId=true" is invoked. This is because of the regexp used to...

Assembly statistics

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Hi, thanks for this tool, already incorporated it into one of our pipelines. That said, I think it currently does not output an assembly statistic file, like Spades does? This...

[FEATURE] Haplotype aware effect prediction

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# nf-core/sarek feature request ## Is your feature request related to a problem? Please describe Typical effect prediction (SNPEff, VEP) will not take into consideration variants "in phase", i.e. each...

### Description of the bug Currently, Sarek produces BAM files for variant calling through the GATK best-practices, including recalibration (default). For DeepVariant, this is discouraged, as stated by the developers:...

align2hints.pl constructs incorrect stop hints for SPALN evidence

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Hi, when parsing SPALN models with align2hints.pl, both the start AND the stop hint are computed from the first cds feature, producing invalid stop hints - and that can lead...

PBSpro wrapper, missing option

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Hi, sorry, pbspro issues again ;) The following line should be added to the wrapper: # PBS -V This will automatically export environment variables. Otherwise, one would have to always...

BAM versus CRAM index extension pattern

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GATK Version 4.0.9.0 What is the issue: When using the -OBI flag in e.g. ApplyBQSR, GATK uses an inconsistent pattern for adding index extensions When using BAM format as output:...

Hi, since I was missing some of the binaries that should be compiled together with cactus (hal package - later figured out that they were in the subfolder submodules/hal/bin), I...

Segmentation result dubious?

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Hi, I am still fighting with this tool to get a reliable workflow sorted out. I am now doing this very slowly, by hand - against a chip-validated cohort. I...

Hi, apologies for using this route, but I am quite stuck with my processing and cannot find a straight answer elsewhere. What is the issue? ============ I have clinical exomes,...