User: FGV

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FGV120
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Posts by FGV

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Comment: C: GNU parallel command with several multiple arguments
... nice trick. :) Thanks, ...
written 10 weeks ago by FGV120
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Comment: C: GNU parallel command with several multiple arguments
... thanks, that worked! But can you explain a bit more the logic behind it? I tried using `-N 2` but with `{1} {2} {3}`, and that did not work. Why does it work with `{4}`? thanks ...
written 10 weeks ago by FGV120
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GNU parallel command with several multiple arguments
... Dear all, I am trying to use gnu parallel to run a command, where each command uses one from the first argument and two from the second. I've tried several things but without success. I'd like to have something like: parallel "command -t {1} {2} {3} > {1}_{2/..}.out " ::: 4 8 ::: File1 Fil ...
parallel gnu parallel written 10 weeks ago by FGV120 • updated 10 weeks ago by ole.tange3.9k
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Merge VCF INFO tags
... Dear all, I have a VCF file that, after annotation from VEP and extraction of tags with `bcftools +split-vep` ends up like: `[...]|amr|4.05357e-01||0|-0.143||||||;gnomADg_AF=0.341347,0.341347;[...]` Is there any way to merge the `gnomADg_AF` tag? For example, choose the MIN() or MAX(), so that ...
vcf tags info written 8 months ago by FGV120
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Comment: A: filter VCF based on info field that has a key but no value
... Have you tried: `bcftools view -e 'IMPUTED' my_fav.vcf.gz` or `bcftools view -i 'IMPUTED' my_fav.vcf.gz` ...
written 8 months ago by FGV120
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Annotate VCF on specific transcripts (ANN field)
... Dear all, I've been using snpEff and snpSift for a while to annotate and filter my VCF files. Usually I just annotate my VCF with snpEff but, as it is, snpEff annotates all transcripts. Recently I wanted to restrict my annotations (ANN) to a list of ~150 transcripts, but could not find a way to do ...
vcf snpsift snpeff written 23 months ago by FGV120 • updated 23 months ago by Pierre Lindenbaum131k
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Query UCSC Browser
... Dear all, I'm trying to query the UCSC database directly from the command line (or R) to get the conservation (e.g. phastCons46wayPrimates) score for a single position. I tried using the Table Browser, and it worked fine: track type=wiggle_0 name="Primate Cons" description="Primate Conservati ...
api ucsc written 2.2 years ago by FGV120
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Answer: A: Paired-end and single-end reads combined during RNAseq - acceptable?
... For a de-novo assembly PE reads are actually the most informative and it is usually advisable to have several PE libraries with different insert sizes (e.g. [here][1]) You can combine together PE and SE reads and there are several programs that allow for it (e.g. Velvet). You can also get some mor ...
written 2.2 years ago by FGV120
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Answer: A: Mapping scaffolds to chromosomes
... How big are the genomes? If small you can try MAUVE or MUGSY... I needed to align some bird genomes a while ago, and in the end had to use MULTIZ. It is a bit of a pain to use but it the end it worked. You might also be interested in looking into [minimap2][2] or [cactus][1]. I've never used any o ...
written 2.2 years ago by FGV120
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Answer: A: How can I make GATK fasta alternate reference maker faster
... I'd suggest splitting your analysis by chromosome/scaffold/contig (or a group of them), and running each one of them in parallel. In the end you can just concat all the files. However, be careful with GATK FastaAlternateReferenceMaker, since it will only replace on the reference alternate alleles o ...
written 2.2 years ago by FGV120

Latest awards to FGV

Popular Question 8 months ago, created a question with more than 1,000 views. For Samtools Vcf Reference And Alternate Alleles
Great Question 20 months ago, created a question with more than 5,000 views. For Fit Mixture Of Gamma And Negative Binomial Distributions In R
Popular Question 23 months ago, created a question with more than 1,000 views. For Samtools Vcf Reference And Alternate Alleles
Scholar 2.2 years ago, created an answer that has been accepted. For A: GNU parallel error: Command line too long
Popular Question 7.6 years ago, created a question with more than 1,000 views. For Fit Mixture Of Gamma And Negative Binomial Distributions In R
Popular Question 7.6 years ago, created a question with more than 1,000 views. For Implement Bgzip Into C Program
Popular Question 7.6 years ago, created a question with more than 1,000 views. For Samtools Vcf Reference And Alternate Alleles
Popular Question 7.6 years ago, created a question with more than 1,000 views. For Simulate Ngs Mapped Reads

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