User: bioguy24

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bioguy24190
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Chicago
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4 months, 2 weeks ago
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Posts by bioguy24

<prev • 233 results • page 1 of 24 • next >
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Haplotypecaller indel realignment
... Is there a way to disable indel realignment in haplotypecaller or is that determained bu the -minPruning? If i am sequencing germline what is recomended? Thanks :) ...
haplotypecaller written 4 months ago by bioguy24190
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Comment: C: sugesstions to optimize an abra2 command
... Thank you very much :). ...
written 4 months ago by bioguy24190
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sugesstions to optimize an abra2 command
... Looking to speed up abra2 and added libIntelDeflater.so and --threads 8/16. I am running diploid germline but don't see how to adjust the pruning to .10 as suggested. Anything else? Thank you :). java -Xmx16G -jar $abra -Dsamjdk.intel_deflater_so_path= --in --out --ref --threads 8 --targets ...
abra2 written 4 months ago by bioguy24190
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Comment: C: processing in strelka2 with multiples bam file in directory
... I changed the shebang line in the python executable to #!/usr/bin/env python to match the other .py on my system and get the below error. python --version on centos 7 Python 2.7.5 echo "${path_to_strelka}/bin/configureStrelkaGermlineWorkflow.py $(for f in *dups.bam; do echo -n "--b ...
written 5 months ago by bioguy24190
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Comment: C: processing in strelka2 with multiples bam file in directory
... The -m and -j are options in the github site but are not reconized. Thank you :). echo "${path_to_strelka}/bin/configureStrelkaGermlineWorkflow.py $(for f in *dups.bam; do echo -n "--bam ${f} "; done;) --referenceFasta ${fasta} --callRegions ${bed} --exome --runDir ${dir} ${dir}/runWorkflow.py ...
written 5 months ago by bioguy24190
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Comment: C: processing in strelka2 with multiples bam file in directory
... I apologize for mis-reading the post and appreciate the help. The same bam file seems to be used in the echo statement and the xargs sh gives the below error. Thank you very much:). echo "${path_to_strelka}/bin/configureStrelkaGermlineWorkflow.py $(for f in *dups.bam; do echo -n "--bam ${bam} ...
written 5 months ago by bioguy24190
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Comment: C: processing in strelka2 with multiples bam file in directory
... The command with the typo in the bam extention: echo -n "${path_to_strelka}/bin/configureStrelkaGermlineWorkflow.py $(for f in duplicate.bam; do echo "--bam ${f} "; done;) --referenceFasta $genome --callRegions $bed --exome --runDir ${abra_dir} ${abra_dir}/runWorkflow.py -m local -j 20" | x ...
written 5 months ago by bioguy24190
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Comment: C: processing in strelka2 with multiples bam file in directory
... I added the echo -n and get the same as above when the | xargs sh is added. The echo -n without looks good. Thank you for your help :). ...
written 5 months ago by bioguy24190
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Comment: C: processing in strelka2 with multiples bam file in directory
... Here is the output: strelka2 v2.9.10.centos6_x86_64, with python --version Python 2.7.5 echo "${path_to_strelka}/bin/configureStrelkaGermlineWorkflow.py $(for f in duplicate; do echo "--bam ${bam} "; done;) --referenceFasta $genome --callRegions $bed --exome --runDir ${abra_dir ...
written 5 months ago by bioguy24190
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Comment: C: processing in strelka2 with multiples bam file in directory
... Things look good untill the | xargs sh then I get: /usr/local/bin/strelka-2.9.10.centos6_x86_64/bin/configureStrelkaGermlineWorkflow.py: line 27: syntax error near unexpected token `(' /usr/local/bin/strelka-2.9.10.centos6_x86_64/bin/configureStrelkaGermlineWorkflow.py: line 27: `if sys.ver ...
written 5 months ago by bioguy24190

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