User: miles.thorburn

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Posts by miles.thorburn

<prev • 16 results • page 1 of 2 • next >
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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 4 weeks 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 4 weeks 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 3 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 3 months ago by miles.thorburn10 • updated 3 months ago by Pierre Lindenbaum108k
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Comment: C: Multiple Sequence Alignment for very large data sets
... Thanks, I'll have a look into these now. ...
written 4 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 4 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 4 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 4 months ago by miles.thorburn10
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Comment: C: Changing Chromosome Notation in Bam Files to Include Sample ID
... Thanks for your suggestions. I've finally come up with a solution, and it was so much easier than I had anticipated. You can directly edit the header of the consensus fasta sequence, which is apparently retained when converting to .phylip. All you need to do is keep a spreadsheet with the informatio ...
written 4 months ago by miles.thorburn10
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Comment: C: Changing Chromosome Notation in Bam Files to Include Sample ID
... Apologies for the lack of information. Ultimately I am going to be converting these files into .phylip format to use in the program VariScan. Unfortunately, there don't appear to be any direct conversions, so I have to convert the file into .fasta first. For VariScan I need anywhere from 12 to 66 ...
written 4 months ago by miles.thorburn10

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