User: curious

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curious220
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Posts by curious

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Comment: C: conda/bioconda installation of plink fails
... I don't know, the idea of environments is to keep things isolated so you don't get conflicts. Trying in a fresh environment is like the equivalent of "did you try turning it off and on again" ...
written 7 days ago by curious220
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Answer: A: conda/bioconda installation of plink fails
... try a a fresh enviornment with conda `conda create -n new_env`. If not activated then probably `conda activate new_env` then try to install. Otherwise maybe google plink binary and download newest if you cna't get conda to work. ...
written 7 days ago by curious220
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Comment: C: Which of the 4 SureSelect Agilent BED files to use with GATK haplotype caller?
... Well not anymore! I'll take a look thanks again. GATK is amazing resource, kind of complicated though. ...
written 9 days ago by curious220
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Comment: C: Which of the 4 SureSelect Agilent BED files to use with GATK haplotype caller?
... I wonder if that even matters for my application, as far as I can tell the bed file is supplied as a argument to GATK Haplotype caller just to cut down on searching time by pointing to specific intervals. I hate making assumptions though i'll be on the lookout ...
written 9 days ago by curious220
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Comment: C: What Agilent Interval Files (.Bed) Should I Use For Exome Variant Calling With G
... Why is this, is this because you can enrich pretty effectively for sequences that are 100bp on wither side of the probe because of some kind of overhang effect? ...
written 9 days ago by curious220
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Which of the 4 SureSelect Agilent BED files to use with GATK haplotype caller?
... I have some BAMs from whole exome sequencing. I want to run GATK haplotype caller, which requires one bed file as input SureSelect kit for the BAMs comes with 4 different .bed files: `*_Covered.bed` `*_AllTracks.bed` `*_Padded.bed` `*_Regions.bed` Googling shows this question has been asked m ...
variant calling gatk sureselect written 9 days ago by curious220
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Is it a convention for displaying human males in VCF as homozygous diploid?
... This isn't beagle specific but I was reading beagle's manual and see: > "At present, version 4 requires haploid male X-chromosome genotypes to > be coded as homozygous diploid genotypes." I started wondering, is showing males as homzygous diploid in VCFs a convention? Or at least common? It ...
vcf diploid written 10 days ago by curious220
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Comment: C: Creating a GenomicsDBImport from the normal Mutect2 calls
... There is another command to combine gvcfs, I used that instead of making a db, but in the end I didn't need a db. I dont know if a workaround is possible What is your actual command and what version are you running. I did get the db to be made successfully ...
written 10 days ago by curious220
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Comment: C: Good quality control metrics to look out for when someone gives you BAMs
... Thank you very much! ...
written 10 days ago by curious220
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Comment: C: how to find haplotype of SNPs
... In VCF specification 0 is ref. I'm not sure if you can phase with 3 SNPs, somebody else will know though ...
written 11 days ago by curious220

Latest awards to curious

Scholar 7 days ago, created an answer that has been accepted. For A: conda/bioconda installation of plink fails
Commentator 8 months ago, created a comment with at least 3 up-votes. For C: Bioinformatics Workstation Suggestions
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Hardware requirement for RNA-seq

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