User: sara.aglantarek

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3 months ago
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6 months, 4 weeks ago
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s**************@studio.unibo.it

Posts by sara.aglantarek

<prev • 13 results • page 1 of 2 • next >
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Comment: C: R: pedigree analysis
... OK got it. Thank you! ...
written 4 months ago by sara.aglantarek10
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Comment: C: R: pedigree analysis
... Actually the regular ped file format is like this... dadid and momid has to be on the same row of the proband, because the proband have to be linked to the parents ids for kinship2 to recognize it as a family. And 0 in the row of dad and mom. ...
written 4 months ago by sara.aglantarek10
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R: pedigree analysis
... Hi everyone! I'm asking a question related to R. I'm not an R user, but it's the only tool that can get me this done. I'm uploading to R a pedigree file that looks like this: famid id dadid momid sex pheno EPBL-0001 epbl0001 epbl0003 epbl0002 2 2 EPBL-0001 epbl0002 0 0 2 1 EPBL- ...
R pedigree kinship2 written 4 months ago by sara.aglantarek10 • updated 4 months ago by zx87549.4k
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Comment: C: Relatedness inference using KING
... Ok I understand that from the ped and the map file I have to create the binary ped (bed, bim, fam). I tried to do this but I get this error: Error: Line 1 of .ped file has fewer tokens than expected. But the ped file has exactly the 6 mandatory columns that should have. How can I solve this pro ...
written 5 months ago by sara.aglantarek10
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Comment: C: Merging VCF files into one
... Thank you Kevin, I really appreciate your patience. It really was a format issue. I did the joint calling on the vcfs and created a unique file containing all of them. Let's see how it works. ...
written 5 months ago by sara.aglantarek10
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Relatedness inference using KING
... Hi everyone! I need some help on KING. I have a multivcf, containing informations about a certain number of trios and I want to confirm the relationship of the trios: so parent-proband = 1st degree, parent-parent = unrelated/2nd degree (if they're consanguineous) etc... I have the pedigree file whi ...
genome next-gen tool snp sequencing written 5 months ago by sara.aglantarek10 • updated 5 months ago by zx87549.4k
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Comment: C: Merging VCF files into one
... Yeah i figure that out, and I don't know why I get this kind of error. I'm running it on the HPC (32 core) of the hospital. ...
written 5 months ago by sara.aglantarek10
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Comment: C: Merging VCF files into one
... Blood samples have been sequenced using Illumina sequencers and whole exome sequencing technology. Sequences have been aligned and variants called using GATK pipeline. Do you have knowledge about the KING software for relatedness inference? I'm supposed to use it after the merging step and I should ...
written 5 months ago by sara.aglantarek10 • updated 5 months ago by Kevin Blighe61k
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Comment: C: Merging VCF files into one
... yes of course, I was just viewing them, also so I can post them easily (I'm viewing them only tab delimited). I'm working form terminal, but since there are many columns, the lines are overlapping. Yeah, I figured out they are missing calls. So can I leave them? They won't mess with the running of ...
written 6 months ago by sara.aglantarek10
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Comment: C: Merging VCF files into one
... So I tried with vcf-merge and bcftools, but since I've never worked with vcfs I don't know what a multi-vcf should look like. Could you please help me? This is the output using vcf-merge. Looks like some fields aren't in the right place. [vcf-merge output][1] And this is the output with bcftools. ...
written 6 months ago by sara.aglantarek10

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