User: graeme.thorn
graeme.thorn • 50
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Posts by graeme.thorn
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... 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 . ...
written 5 weeks ago by
graeme.thorn • 50
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... 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.thorn • 50
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... 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.thorn • 50
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... 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 ...
written 6 weeks ago by
graeme.thorn • 50
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... 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. ...
written 10 weeks ago by
graeme.thorn • 50
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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.thorn • 50
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... 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 ...
written 3 months ago by
graeme.thorn • 50
• updated
3 months ago by
Kevin Blighe ♦ 63k
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... 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.thorn • 50
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... 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 ...
written 3 months ago by
graeme.thorn • 50
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... 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 ...
written 4 months ago by
graeme.thorn • 50
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