User: samuel.lipworth

Reputation:
10
Status:
New User
Location:
University of Oxford
Last seen:
1 day, 6 hours ago
Joined:
7 months, 3 weeks ago
Email:
s**************@medsci.ox.ac.uk

Academic junior doctor in Oxford - attempting to learn bioinformatics for microbiology.

Posts by samuel.lipworth

<prev • 18 results • page 1 of 2 • next >
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vcf-consensus wrong bases
... Hi I have a vcf file from which I am calling: vcf-consensus filtered.vcf.gz < NC000962.fasta > test.fasta There are bases in the new test.fasta which are different from the reference but not called as SNPs in filtered.vcf.gz - how can this be!? The VCF file is correct but I don't understand ...
vcf fasta snp written 2 days ago by samuel.lipworth10
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Answer: A: vcf at variable sites only
... Grep is the answer, sorry please close this question! ...
written 10 weeks ago by samuel.lipworth10
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vcf at variable sites only
... Hi, I have a vcf file which simply gives the call at every single position eg: L=C;BaseCounts=4,131,2,5;BaseCounts4=0,92,0,0;DM4=0.037;DM4L=-2.134;DP=147;DP4=47,45,0,0;DPT4L=-14.831;DZ4=0.052;DZ4L=-2.141;GC=57.430;MQ=60;MQ4=60;PCALL4=1.000;PCONS4=1.000;SBR=0 GT:DP 0/0:92 R00000039 7336 . T ...
vcf written 10 weeks ago by samuel.lipworth10
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(Closed) convert between vcf types
... I currently a vcf file which describes in one file the variant call for all samples at all variable positions eg: sample1, sample2, sample3, sample4, sample5 1 A A T A T 5 T T G T G I want to convert to the vcf type which shows the call for a variable positions for one sample ...
vcf written 11 weeks ago by samuel.lipworth10 • updated 11 weeks ago by Pierre Lindenbaum96k
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list variants from concatonate snp alignment
... Hi so I have a snp alignment and I would like to use some software to classify all of my samples into a group eg 0 or 1 depending on whether they have the wild type or mutant base at any given variable site. eg sample 1 (wild type) actga Sample 2 (query) accgg so sample 2 wou ...
phylogeny python snp written 4 months ago by samuel.lipworth10 • updated 4 months ago by Pierre Lindenbaum96k
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Comment: C: Clusters of max SNP distance
... Sure: a matrix of snp distances between 4 samples eg. 0 500 0 34 4 0 19 20 3 0 So i can obviously reconstruct the phylogeny using eg ML which would show me that there is a reconstructed snp distance of <12 between samples 3 and 2, and also 4 and ...
written 5 months ago by samuel.lipworth10
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Clusters of max SNP distance
... Hi, I want to find all clusters of a max SNP distance of say 12 snps of 500 samples. I have a data matrix showing the SNP distances but need an algorithm to cluster them - something like hierarchical clustering with a termination at maximum distance of 12 but I'm not sure how to do this in eg R. A ...
R snp written 5 months ago by samuel.lipworth10 • updated 5 months ago by Petr Ponomarenko2.4k
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Comment: C: Analyse VCF file to find snps common to all samples in lineage
... so for example I have 22 bacterial genomes which I know from creating a snp based phylogeny tree cluster into 7 distinct lineages. I can see what these snps are on a core genome alignment multi-fasta file but this is obviously a very slow way to do it so I want to try to get this information from t ...
written 6 months ago by samuel.lipworth10
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Analyse VCF file to find snps common to all samples in lineage
... I have a VCF file with 22 different samples in it. Looking at the example below I know that all of the 2s come from the same lineage from looking at my phylo tree. What can I use to query the vcf so that I can group different isolates from the same lineage together and find out when there is a SNP ...
vcf snp written 6 months ago by samuel.lipworth10 • updated 4 months ago by Pierre Lindenbaum96k
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VelvetK long Kmers
... I have been using velvetK to estimate optimal Kmer lengths and then plugging these into velvet optimiser. When I then annotate these assemblies (using Prokka) and stick them through Roary, they seem to group by assembly length rather than true phylogeny. I know the reads are not nonsense because w ...
velvetoptimiser velvet denovo assembly written 6 months ago by samuel.lipworth10

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