User: felipead66

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felipead6620
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Posts by felipead66

<prev • 11 results • page 1 of 2 • next >
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Comment: C: snp identification with Haplotypecaller and SelectVariants
... How to extract gvcf from haplotype caller? ...
written 9 hours ago by felipead6620
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snp identification with Haplotypecaller and SelectVariants
... I want to find the snps for 10 cultivars of almond. Which of the following is correct: 1. Use haplotypecaller to find snps for each cultivar (based on the reference genome), then use selectvariants to find true snps and finally filter the snps with variant filter or 2.Use haplotypecaller to find ...
gatk snp written 5 days ago by felipead6620 • updated 5 days ago by Pierre Lindenbaum118k
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Comment: C: VariantFiltration warning "undefined variable"
... Actually there is, that is why i wonder ...
written 5 days ago by felipead6620
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Comment: C: VariantFiltration warning "undefined variable"
... #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT tredna_sm gene.1 1039 . C T 107.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.293;DP=40;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=51.55;MQRankSum=-3.589;QD=2.76;ReadPosRankSum=0.097;SOR=0.446 GT:AD:DP:GQ:PL 0/1:33,6:39:99:136,0,4437 gene.1 10 ...
written 5 days ago by felipead6620 • updated 5 days ago by Pierre Lindenbaum118k
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VariantFiltration warning "undefined variable"
... when i run ./gatk VariantFiltration -R genome.fasta -V vcf_file.vcf -o outfit_vcf.vcf --filter-expression "QD <2.0" --filter-name "qdthres" I get a warning: undefined variable QD. The same happens when I use MQ, FS, MQRankSum. ...
gatk variantfiltration error written 6 days ago by felipead6620 • updated 6 days ago by Pierre Lindenbaum118k
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Comment: C: Annovar annotation for plants
... I did run VEP but as a consequence i only get "intergenic_variants". I assume something is wrong with the entire run but I cannot figure out what. ...
written 13 days ago by felipead6620
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Comment: C: Bio-DB-HTS installation and ensembl-vep
... Even using cpan, I still get an error. Should I use cpan inside ensembl-vep folder? Alternatively, how to add it to PERL5LIB? Edit: I am in Ubuntu ...
written 26 days ago by felipead6620
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Comment: C: Bio-DB-HTS installation and ensembl-vep
... I installed it both manually from https://github.com/Ensembl/Bio-DB-HTS and as @cmdcolin suggested i run "cpan Bio::DB::HTS" and seems to work, since I get Bio::DB::HTS is up to date (2.11) How should I tell VEP how to find it? ...
written 26 days ago by felipead6620
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Comment: C: Bio-DB-HTS installation and ensembl-vep
... Thank you for your suggestion. I run "cpan Bio::DB::HTS" and I get Bio::DB::HTS is up to date (2.11) but still when installing vep and run "perl INSTALL.pl" I get the following: This module requires htslib (http://htslib/org) Install it if you have not done so already. This script will attempt ...
written 26 days ago by felipead6620
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Bio-DB-HTS installation and ensembl-vep
... I want to use ensembl-vep with custom annotation. In order to use gff file I need to have library Bio-DB-HTS installed. I downloaded Bio-DB-HTS and used Build.PL with no errors. When I try to install ensembl-vep it still gives an error asking for Bio-DB-HTS library. How should I install Bio-DB-HTS ...
bio-db-hts vep ensembl written 27 days ago by felipead6620 • updated 27 days ago by Emily_Ensembl17k

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