User: raf.marcondes

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Posts by raf.marcondes

<prev • 18 results • page 1 of 2 • next >
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merging VCFs with non-overlapping sets of variants but partially overlapping sets of samples
... How can I merge VCFs files with non-overlapping sets of variants but partially overlapping sets of samples? For example because for a certain chromosome I only had coverage for some but not all of my samples. I can find tools to merge VCFs with identical sets of variants but non-overlapping samples ...
vcf written 4 weeks ago by raf.marcondes40 • updated 4 weeks ago by Pierre Lindenbaum134k
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Merging genomic databases from different intervals (GenomicsDBImport)
... Hi all. I'm trying to put a large dataset through GenomicsDBImport, but it's not finishing within my cluster's 72 hr kill time. I know I can make this more efficient by running different parts of the genome simultaneously using -L to specify intervals. But I don't see a tool to merge the resulting i ...
gatk written 7 weeks ago by raf.marcondes40
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Comment: C: Trouble installing/running GEMMA
... yup ...
written 5 months ago by raf.marcondes40
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Trouble installing/running GEMMA
... Hi all, I succesfully (?) installed GEMMA with conda but am getting an error when I try to run it: (base) a4-d1-8c-60-8d-82:~ Rafael$ gemma dyld: Library not loaded: @rpath/libgfortran.4.dylib Referenced from: /opt/anaconda2/bin/gemma Reason: image not found Abort trap: 6 I already tried rei ...
gemma written 5 months ago by raf.marcondes40
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Liftover nonmodel VCF
... Hi all, I have a FASTA genome assembly and a VCF for my (nonmodel) study species. Now I want to liftover the VCF to the Zebra Finch genome (https://www.ncbi.nlm.nih.gov/assembly/GCF_003957565.1). I've found Picard LiftOver GATK and CrossMap, but both require a UCSC chain file, which apparently can o ...
chain file satsuma liftover ucsc written 6 months ago by raf.marcondes40
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Comment: C: Satsuma output format to chain format
... I know this was a long time ago, but anyone goy any thoughts? I'm hoping to do the same thing. ...
written 6 months ago by raf.marcondes40
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"Illegal instruction" error in BCF tools
... Hi all, When I run the following command in in interactive session in my HPC system, it seems to run fine. I let it go for a minute or so, which it does without errors, and then kill it, because it's not appropriate to run such job in an interactive session. But when I submit it as a batch job, it ...
bcftools written 10 months ago by raf.marcondes40
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How to use gathervcfs in GATK 4.1.4.0
... Hi all, I used GenomicsDBImport to generate a genomic database from a bunch of gvcf files corresponding to a number of genomic intervals. For each interval, GenomicsDBImport produced a directory with contents that look like this: [rmarcondes@boslogin02 db_180]$ pwd /n/holyscratch01/edwards_ ...
gathervcfs written 11 months ago by raf.marcondes40
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Error in GATK GenomicsDBImport
... Hi, I have a large number of gvcf files that I'm trying to joint genotype, by first running GenomicsDBImport in GATK 4.1.4.0. When I say large I mean 135 samples * 229 genomic intervals = 30,915 files. Here's what I have: java -Xmx80g -XX:ParallelGCThreads=20 -jar $GATKPATH GenomicsDBImport - ...
gatk genomicsdbimport written 11 months ago by raf.marcondes40 • updated 4 months ago by yussab10
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Use of GATK HaplotypeCallerSpark
... Hi all, I wanted to post this question to the GATK support forum, but I can't for the life of me figure out how to do it, so here it goes. How bad exactly is it to use HaplotypeCallerSpark in GATK 4.0.2.1? I realize it's in beta, but I'm wondering if that means "your results will be useless" or ju ...
gatk written 16 months ago by raf.marcondes40

Latest awards to raf.marcondes

Great Question 4 months ago, created a question with more than 5,000 views. For bwa: fail to locate the index files
Popular Question 9 months ago, created a question with more than 1,000 views. For Pararellization in GATK 4
Student 11 months ago, asked a question with at least 3 up-votes. For Pararellization in GATK 4
Popular Question 21 months ago, created a question with more than 1,000 views. For bwa: fail to locate the index files

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