User: felipead66
felipead66 • 20
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Posts by felipead66
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... How to extract gvcf from haplotype caller? ...
written 9 hours ago by
felipead66 • 20
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... 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 ...
written 5 days ago by
felipead66 • 20
• updated
5 days ago by
Pierre Lindenbaum ♦ 118k
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... Actually there is, that is why i wonder ...
written 5 days ago by
felipead66 • 20
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... #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
felipead66 • 20
• updated
5 days ago by
Pierre Lindenbaum ♦ 118k
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6 follow
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... 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. ...
written 6 days ago by
felipead66 • 20
• updated
6 days ago by
Pierre Lindenbaum ♦ 118k
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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
felipead66 • 20
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... 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
felipead66 • 20
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... 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
felipead66 • 20
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... 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
felipead66 • 20
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... 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 ...
written 27 days ago by
felipead66 • 20
• updated
27 days ago by
Emily_Ensembl ♦ 17k
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