User: graeme.thorn

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graeme.thorn50
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Posts by graeme.thorn

<prev • 53 results • page 1 of 6 • next >
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Fixing genotypes from split vcf
... I have split a multi-sample vcf into each sample, and I was wondering if there was a simple method for fixing the genotype for variants to 0/1 for each single-sample vcf, and changing the alternate allele to match the new genotype. For instance, if the vcf contains a read like ` chr1 945122 . ...
vcf written 5 weeks ago by graeme.thorn50
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Comment: C: GATK VariantFiltration multiple filters including genotype for multi-sample VCF
... Thanks! A quick test has shown that variations of this (see the answer) are what I required. The GATK help pages don't seem that helpful. ...
written 6 weeks ago by graeme.thorn50
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Answer: A: GATK VariantFiltration multiple filters including genotype for multi-sample VCF
... As per @Pierre Lindenbaum's comment above, the correct filter for the genotype is ````vc.getGenotype("SAMPLEn").isHomRef()```` to select the "0/0" genotype and ````!vc.getGenotype("SAMPLEn").isHet() && !vc.getGenotype("SAMPLEn").isHomVar()```` to select the "0/0" or "./." genotypes. This c ...
written 6 weeks ago by graeme.thorn50
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GATK VariantFiltration multiple filters including genotype for multi-sample VCF
... I have a multisample VCF and I want to filter it based on: 1. The sequencing depth from the first sample (which is a germline sample) and 2. The genotype of the first (and/or the third) samples (which are both germline samples) I've been investigating ````gatk VariantFiltration```` for doing thi ...
vcf gatk written 6 weeks ago by graeme.thorn50
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Variant data from covid-19 patients
... Are there any resources with summarised variant data from covid-19 patients who have had their genomes sequenced? The underlying sequencing data is not required, just the called variants. There are plenty of resources with viral genomes but nothing from the patients suffering from covid-19. ...
vcf covid-19 written 10 weeks ago by graeme.thorn50
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Comment: C: RNAseq and PAM50 prediction
... Thanks Kevin, but this is work in collaboration with a commercial company who will be running PAM50 on the non-deduplicated data (the sequencing included UMIs, which we are taking into account, and they aren't), so I was looking for the most robust way of running PAM50 on the data so we can do a dir ...
written 3 months ago by graeme.thorn50
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RNAseq and PAM50 prediction
... I've a set of RNAseq data from breast cancer tissue samples (counts and post-cqn-normalised log(RPKM) values) and wish to use the PAM50 classifier to classify them. I've seen the question https://www.biostars.org/p/335640/ and the question https://www.biostars.org/p/102212/, and neither are particu ...
genefu R rna-seq written 3 months ago by graeme.thorn50 • updated 3 months ago by Kevin Blighe63k
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Comment: C: Downloading hg38 centromere and telomere positions from UCSC table browser
... I will provide feedback to them about this. However, I'm just looking for a table of positions in hg38 that I can bolt on to the existing removed regions to ease the workflow. EDIT: it does look like this is a frequent question to them, see for instance here: https://groups.google.com/a/soe.ucsc.ed ...
written 3 months ago by graeme.thorn50
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Downloading hg38 centromere and telomere positions from UCSC table browser
... I'm converting an R code (from here: https://github.com/cancer-genomics/delfi_scripts) from hg19 to hg38 assembly, and it relies on automatically downloading telomeric and centromeric regions from the UCSC table browser: genome <- "hg19" mySession <- browserSession() genome(mySes ...
genome R ucsc written 3 months ago by graeme.thorn50
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Extracting variant reads and reference reads quickly from mapped files
... As per the question, I want to check whether the effect seen here in this paper: https://www.ncbi.nlm.nih.gov/pubmed/30404863 is true for my samples (the effect that fragments of cfDNA containing tumour-specific variants are shorter than those that don't, indicating the tumouric origin of those frac ...
dna-seq variant written 4 months ago by graeme.thorn50

Latest awards to graeme.thorn

Popular Question 9 weeks ago, created a question with more than 1,000 views. For Error in GSNAP - unable to find genome in directory
Scholar 9 months ago, created an answer that has been accepted. For A: Error in GSNAP - unable to find genome in directory
Popular Question 14 months ago, created a question with more than 1,000 views. For Error in GSNAP - unable to find genome in directory
Scholar 16 months ago, created an answer that has been accepted. For A: Error in GSNAP - unable to find genome in directory
Popular Question 21 months ago, created a question with more than 1,000 views. For Error in GSNAP - unable to find genome in directory
Scholar 22 months ago, created an answer that has been accepted. For A: Error in GSNAP - unable to find genome in directory
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: TCGA (legacy) barcodes for identifying tumour/normal samples
Scholar 2.0 years ago, created an answer that has been accepted. For A: Error in GSNAP - unable to find genome in directory
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Error in GSNAP - unable to find genome in directory
Scholar 4.6 years ago, created an answer that has been accepted. For A: Error in GSNAP - unable to find genome in directory

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