User: bioinformatics98

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Posts by bioinformatics98

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BASH Finding Common Elements
... Hello! What is the best way to find common elements between 2 columns using BASH? ...
bash written 9 weeks ago by bioinformatics980 • updated 9 weeks ago by Joe18k
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Comment: C: Vcfanno bgzf error
... I am not sure how it was compressed as I got it from here: https://github.com/brentp/vcfanno When I tried running this example/exac.vcf.gz on Brentp's example input file called query.vcf.gz --> my code worked perfectly! I did exactly how it says to do under the "Example" section of Brentp's githu ...
written 8 months ago by bioinformatics980
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Vcfanno bgzf error
... Hello all, Whenever I run vcfanno on my samples, I get this error: vcfanno.go:115: found 12 sources from 3 files vcfanno.go:156: falling back to non-bgzip api.go:796: bix: error opening bgzf reader for example/exac.vcf.gz: bgzf: could not determine block size Can somebody please expla ...
vcfanno written 8 months ago by bioinformatics980
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Command for Running Vcfanno Software
... Hello all, I am trying to run Vcfanno (https://github.com/brentp/vcfanno) on the example data they have given, and I do not know what my command should be. I tried their suggested: ./vcfanno -lua example/custom.lua example/conf.toml example/query.vcf.gz and also: vcfanno -lua example/c ...
vcfanno written 8 months ago by bioinformatics980
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Seqmule Command Line Explanation
... Hello, Can somebody please help me understand what the command here is doing: JOBID=0 PID=164655 command=/home/CLSTR/user/software/seqmule/bin/secondary/../../bin/secondary/worker /home/CLSTR/user/data/sample/seqmule.02262020.153477.logs 31 "/home/CLSTR/user/software/seqmule/bin/second ...
seqmule written 9 months ago by bioinformatics980
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GATK genotypemergeoption Error
... Hi all, I am trying to run a single sample dataset of a paired-end sample obtained for exome sequencing (Read 1 and Read 2) through the seqmule pipeline and it gives this error: NOTICE: normalzing VCF with Vt... NOTICE: done normalzing. NOTICE: keep variants if they are unfiltered in a ...
gatk seqmule written 9 months ago by bioinformatics980
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Failed to find GenomeAnalysisTKLite.jar file
... Hi everyone, I am trying to run the seqmule pipeline without GATKLite (I want the pipeline to use the full GATK instead) -- I have already removed any command asking for gatklite in the advanced config file of seqmule, however I keep getting this error: [ => SeqMule Execution Status: Runnin ...
seqmule gatklite gatk written 9 months ago by bioinformatics980
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Comment: C: seqmule gatk vcfv4.2 error
... Here you go: JOBID=0 PID=1863 command=/home/CSTR/user/softwares/seqmule/bin/secondary/../../bin/secondary/worker /home/CSTR/user/data/sample/seqmule.02092020.57459.logs 31 "/home/CSTR/user/softwares/seqmule/bin/secondary/../../bin/seqmule stats -tmpdir /tmp -ref /home/FCAM/CSTR/user/softwares/seqmu ...
written 9 months ago by bioinformatics980
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Comment: A: seqmule gatk vcfv4.2 error
... The pipeline is requiring me to use GATKlite -- is there a way I can force it to use GATK instead? ...
written 9 months ago by bioinformatics980
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Comment: C: seqmule gatk vcfv4.2 error
... Ah! Thank you so much! The pipeline is requiring me to use GATKlite (v.2.3-9) -- is there a way I can force it to use GATK instead? ...
written 9 months ago by bioinformatics980

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