User: miles.thorburn

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Posts by miles.thorburn

<prev • 18 results • page 1 of 2 • next >
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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 12 weeks ago by miles.thorburn10
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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 12 weeks ago by miles.thorburn10 • updated 12 weeks ago by h.mon22k
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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 6 months ago by miles.thorburn10
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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 6 months ago by miles.thorburn10
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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 9 months ago by miles.thorburn10
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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 9 months ago by miles.thorburn10 • updated 9 months ago by Pierre Lindenbaum115k
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Comment: C: Multiple Sequence Alignment for very large data sets
... Thanks, I'll have a look into these now. ...
written 9 months ago by miles.thorburn10
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Comment: C: Multiple Sequence Alignment for very large data sets
... There aren't many, but off the top of my head I can think of 2 good examples. We are trying to get away from the candidate gene approach here, and our data set is outstanding. I am reasonably sure each chromosome should be aligned without any problems. ...
written 9 months ago by miles.thorburn10
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Comment: C: Multiple Sequence Alignment for very large data sets
... Ultimately this is a genome wide scan for balancing selection. We would do it at the whole genome level, but in using each individual chromosome separately, we cut down the computational power needed and to cut down the amount of time needed for each step. Make sense? ...
written 10 months ago by miles.thorburn10
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Multiple Sequence Alignment for very large data sets
... What would your recommendations for the best MSA programs for comparing large nucleotide sequences of the same species? My data set consists of 66 individuals from 11 populations. I will be using VariScan to scan for selection next, but need to realign each of the 21 chromosomes separately for each ...
alignment msa written 10 months ago by miles.thorburn10

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