User: cristina_sabiers

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70
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Location:
Spain
Last seen:
1 year, 1 month ago
Joined:
4 years, 5 months ago
Email:
c*****************@gmail.com

Posts by cristina_sabiers

<prev • 172 results • page 1 of 18 • next >
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Comment: C: DE novo call from trio
... Hello Khare sorry, I didnt want to write you back until I perfom again the alignment. this time I used the reference genome from GATK and supporting file from GATK, and run the process from the start. My results are almost the same and dint get any high or lowdenovo variants. ...
written 14 months ago by cristina_sabiers70
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Comment: C: DE novo call from trio
... thanks for your time Khare, I really appreciate it :) I have a last question I could just use my reference genome from ensembl.org and use as --supporting file ftp://ftp.1000genomes.ebi.ac.uk/../../vol1/ftp/release/20130502/phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz.....file ...
written 14 months ago by cristina_sabiers70
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Comment: C: DE novo call from trio
... Ok, but If I use the reference genome from ftp.broadinstitute.org/bundle then I asume I should do the alignment over again from the start with my fastq files right? ( I used from start the reference genome from ensembl.org) Should really affect that point on my results to get high or low denovo va ...
written 14 months ago by cristina_sabiers70
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Comment: C: DE novo call from trio
... Ok, thanks "I am not sure why "convert to biallelic" step is necessary." I followed the tips at gatk forum [CalculateGenotypePosteriors error][1] "What were the hard filtration parameters?" I used this pipeline: [https://gencore.bio.nyu.edu/variant-calling-pipeline/][2] jav ...
written 14 months ago by cristina_sabiers70
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Answer: A: DE novo call from trio
... Thanks for the help Khare :) Its does really matter if you use gvcf format instead vcf? I thought was the same. Will try with -ERC GVCF option. and see if I get any different result. Thanks for the advice. If I use Varscan using mpileup at the end I get similar results. I am just a bit surprised ...
written 14 months ago by cristina_sabiers70
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DE novo call from trio
... Hi! I had done - Alignment - Sorting sam file - Mark duplicates - Realignment call variants - BQSR - Call raw snps and Apply hard filtering Then I merge my three vcf files (dad, mum, child) java -jar GenomeAnalysisTK.jar -T CombineVariants -R hg38.fa --variant sample02.vcf --var ...
exome written 14 months ago by cristina_sabiers70
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why I miss genes in the annotations?
... Hi! Hope someone can clarify me this I downloaded the gtf annotation from http://www.gencodegenes.org/releases/26lift37.html I generated my own bed file for annotate just the gen name on my vcf file, the fact is that I miss a few genes for example this one that don't appear (it does with annovar ...
annotat written 3.3 years ago by cristina_sabiers70
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Comment: C: esearch problem downloading files
... thank you so much! worked with your code. Thanks ...
written 3.3 years ago by cristina_sabiers70
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Comment: C: esearch problem downloading files
... Thank genomax, must be st wrong in the installation or in some crazy way they bann me, will try in my other O.S ...
written 3.3 years ago by cristina_sabiers70
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Comment: C: esearch problem downloading files
... I do something wrong? its like I go to restricted area? Thanks for the help ...
written 3.3 years ago by cristina_sabiers70

Latest awards to cristina_sabiers

Popular Question 3.0 years ago, created a question with more than 1,000 views. For merge vcf file
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Aligning unmapped reads to viral genomes
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