User: lait

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lait150
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Posts by lait

<prev • 84 results • page 1 of 9 • next >
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VCF files never get annotated with PG tag for CalculateGenotypePosteriors
... In our pipeline, we use GATK on whole exome sequencing data consisting of Trios (mother, father and child). We process each sample alone (GVCF is not used and combined genotyping is not applied). All steps from BaseRecalibration to Variants recalibration to finally calling snps and indels are done. ...
gatk calculategenotypeposteriors genotype denovo written 9 months ago by lait150 • updated 7 months ago by Biostar ♦♦ 20
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an efficient way to annotate mutations from vcf files using multiple annotation files
... we do whole exome sequencing at our lab since years, and we already have an established bioinformatics pipeline. Now we are planning to modify/renew our "annotation" step. Two main points should be done: 1. We are planning to annotate the vcf files using Ensembl VEP. 2. Additionally, we have s ...
lovd ensembl clinvar vep cadd written 10 months ago by lait150 • updated 9 weeks ago by Biostar ♦♦ 20
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Comment: C: error bcftools isec
... yes, no spaces are present, I will try bedtools then, thanks for your answer. ...
written 11 months ago by lait150
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error bcftools isec
... I was trying this way [ here][1] to find the intersection between two vcf files. - Vcf file 1: a small vcf file containing some mutations that I am interested in. - Vcf file 2: vcf file for chromosome X from gnomad database, so basically it contains a lot of useful allele frequencies annotatio ...
vcf tabix bcftools written 11 months ago by lait150 • updated 11 months ago by jared.andrews077.6k
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number of cycles, Nextseq500, for whole exoems equencing, which option is more efficient?
... Hi all, we are moving from Illumina Hiseq2500 to Nextseq500 soon. For our Hiseq2500 we had reads of 101 bp length. We mainly use it for whole exome sequencing, and we have a well established pipeline for the full analysis of the WES data. **-1-** - With respect to Nextseq500, my question is: co ...
nextseq hiseq cycles reads-length written 15 months ago by lait150 • updated 15 months ago by toralmanvar900
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Comment: C: EXCAVATOR shows 1 deletion which is not TRUE in IGV
... The coverage of the gene is almost the same acrross the other exons.. EXCAVATOR shows a genotype of 1/1 for that deletion.. actually it shows a genotype of 1/1 for all the detected CNVs, whether it is a deletion or an insertion. Do you recommend another good SV caller for exome data to try if the re ...
written 17 months ago by lait150
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EXCAVATOR shows 1 deletion which is not TRUE in IGV
... Hi, I have WES data for a sample having a specific phenotype. I ran EXCAVATOR on that sample, trying to detect CNVs. I am interested to check deletions happening on gene A, because patients having that specific phenotype would frequently get deletions in that gene A. In EXCAVATOR's results file: ...
exome excavator wes cnv igv written 17 months ago by lait150
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bionano's raw data of images, safe to delete?
... Hi everyone, this question is for those who have worked with bionanogenomics data. Do you think the raw data, which is basically images of points, which are used to produce the molecules, is of any use? each run generates around 1 TB of raw data, and I would like to know if this data would be of an ...
rawdata bionano molecules written 17 months ago by lait150
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Comment: C: bionano hybrid scaffold
... thanks for your answer, that is correct. but do you think WES data could be in any way useful , as a complementary data, for the bionano optical mapping? ...
written 18 months ago by lait150
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bionano hybrid scaffold
... Hi, is it possible to use illumina whole exome sequencing data as input for the hybrid scaffold tool in bionano access software ? I have WES data and bionano assembly data for the same sample. I was wondering if the WES data is enough to be used by the hybrid scaffold tool? Thanks ...
optical mapping wes bionano illumina written 18 months ago by lait150 • updated 18 months ago by WouterDeCoster44k

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