User: miles.thorburn

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Posts by miles.thorburn

<prev • 21 results • page 1 of 3 • next >
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PAML needs branch labels in tree
... I am trying to use PAML for the first time, and it's thrown up a few errors I am struggling to fix. The manual is particularly tricky to read, but I've solved most of the other problems I've come across. I am aiming to use it to calculate dN/dS for sets of genes. I used RAxML to generate my trees in ...
paml newick tree written 5 weeks ago by miles.thorburn40 • updated 11 days ago by Biostar ♦♦ 20
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Answer: A: Filtering VCFs and Phasing
... So I figured it out. Turns out it was simply a misunderstanding of the parameters. inthe VCFTools step, --max-missing needs to be higher than 0.9 (I used 0.95 in the end). I believe this means only variants with a maximum of 5% missing information were allowed to be kept. After testing a few differe ...
written 7 weeks ago by miles.thorburn40
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Filtering VCFs and Phasing
... I have been trying to phase 66 genomes that are all contained in chromosome specific VCF files using the software ShapeIt. I have a working pipeline (works if I use the --force command to override the error I will discuss). I get the following error: *33mERROR: 15611 SNPs with high rates of m ...
shapeit vcf filtering vcftools snp written 7 weeks ago by miles.thorburn40
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Comment: C: PSMC: fq2psmc conversion problems
... Does this mean I'm meant to call variants for each sample individually? I did the variant call altogether, and then extracted each sample from the vcf so each fastq is the whole genome consensus sequence for each individual. I would use MSMC, but we didn't want to get phasing information since thi ...
written 5 months ago by miles.thorburn40
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PSMC: fq2psmc conversion problems
... I am in the process of using PSMC to look at my populations demographic history, but I am having issues with the conversion from fastq to psmcfa. I followed the recommendations as best as I could on the github page (https://github.com/lh3/psmc), though I did my variant call with the entire cohort ...
psmcfa psmc fastq conversion written 5 months ago by miles.thorburn40 • updated 5 months ago by h.mon23k
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Comment: C: No QD scores on 10% of observations in VCF?
... Hi, Correct, you go through HaplotypeCaller, then GenomicsDBImport, and finally into GenotypeGVCF which produces a normal VCF file with all SNPs and Indels from your samples. This is the current recommended GATK pipeline for variant calling. See the workflow [here][1]: [1]: https://gatkforums.b ...
written 9 months ago by miles.thorburn40
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No QD scores on 10% of observations in VCF?
... I am hard filtering my first VCF, and currently exploring the scores to set my thresholds. I'm basing this mostly on the GATK best practises workflow on their website as that's how I've generated all of my VCFs. When I extracted QD (Quality by Depth) scores, I noticed 32573 of the 323529 entries we ...
vcf gatk qd filtering written 9 months ago by miles.thorburn40
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Comment: C: Adding Read Groups to Merged Bams
... Thanks for the speedy response. Damn, such a small oversight on my part to not include '-R' in the BWA script, and weeks of work undone. Thanks for the tool too, but I think I'm going to go back and map the reads again but with the proper read groups. ...
written 11 months ago by miles.thorburn40
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Adding Read Groups to Merged Bams
... Hi all, I am currently processing my .bam files using Picard and GATK. However, I have come across the missing read group error, and realised that I have either lost, or never assigned read group information when using BWA to map my reads to the reference. I have already merged by .bam files for e ...
rg picard read group written 11 months ago by miles.thorburn40 • updated 11 months ago by Pierre Lindenbaum116k
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Comment: C: Multiple Sequence Alignment for very large data sets
... Thanks, I'll have a look into these now. ...
written 12 months ago by miles.thorburn40

Latest awards to miles.thorburn

Scholar 7 weeks ago, created an answer that has been accepted. For A: Filtering VCFs and Phasing
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Filtering VCFs and Phasing

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