Comments (4)
Proposed changes made on s-boardman branch; currently testing before issuing pull request.
from speedseq.
hey @s-boardman , try this out and see if it works for you
from speedseq.
Hi @cc2qe, thanks for looking into this!
I've copied the speedseq & annotate_rd.py scripts to my local install of SpeedSeq and updated the config accordingly. Unfortunately I get the same error with 10000bp windows, but it still works fine with 6000bp ones?
I think those are the only two files I need to copy over? Did you have to recompile the source before it worked for you?
from speedseq.
Yes, those are the only two files you should need to copy over. hang on, let me test further
from speedseq.
Related Issues (20)
- compilation of freebayes module fails on Ubuntu 18.04 HOT 2
- Error -running speedseq SV - missing pair end parameters:mean stdev
- Parallel link is dead HOT 1
- problems about vcf files.
- Warning: --split_bam (-S) is deprecated
- speedseq var and sv only on genomic regions
- Read block operation failed with error HOT 1
- is there a container? HOT 2
- Linker error when doing `make cnvnator`
- -M parameter for BWA MEM alignment
- error: static assertion failed: comparison object must be invocable as const
- Bam file not generated using speedseq align
- mismatched line lengths at line 3 within sequence
- Speedseq is runnning infinitely HOT 1
- [Question] Is ARM64 supported ? HOT 1
- configure: error: cannot guess build type; you must specify one
- error: cannot guess build type; you must specify one
- make :can not find -lCore -lRIO -lHist -lGraf -lGpad -lTree -lMathCore
- Are CRAM files supported by SpeedSeq?
- Compile Errors: *** [Makefile:59: cnvnator] Error 1
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from speedseq.