User: blueskypie

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blueskypie50
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50
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New User
Location:
United States
Last seen:
7 months, 4 weeks ago
Joined:
5 years, 1 month ago
Email:
j*******@gmail.com

Posts by blueskypie

<prev • 13 results • page 1 of 2 • next >
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use `plink --rel-cutoff` to remove related samples
... In the [plink --rel-cutoff][1] option, the default value for genomic relateness is 0.025. How does this genomic relateness value correspond to the [degree of relationship][2] or the PI-HAT? Thanks for any help! [1]: https://www.cog-genomics.org/plink/1.9/distance#rel_cutoff [2]: https://en.wi ...
plink written 8 months ago by blueskypie50 • updated 8 months ago by chrchang5236.5k
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Answer: A: sex imputation based on SNP data
... Thanks for the help, @RamRS! Are you saying that PLINK can run batch processing like `plink file.containing.plink.commands`? Thanks again! ...
written 8 months ago by blueskypie50
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sex imputation based on SNP data
... Hi, is there any **R package** that can do sex imputation from GWAS SNP data? Or is there anyway to run PLINK inside R code? Thanks a lot! ...
sex imputation written 8 months ago by blueskypie50
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Comment: C: fastq reads cleaning
... from what I read briefly, seems fastq, for paired sequencing, will change a base to its corresponding base in the other read of the pair if the corresponding base has much higher quality score. ...
written 11 months ago by blueskypie50
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Comment: C: fastq reads cleaning
... Thanks @genomax for the insight! I'm checking fastp tool, but is a little worried that it may be a bit excessive in cleaning and correction, since it not only removes part of the reads, also makes change to the remaining bases. ...
written 11 months ago by blueskypie50
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Comment: A: fastq reads cleaning
... Thanks for the comment, @JC! Even if those bad reads are kept, won't they be filtered out after mapping? Is there any study to demo that there is a difference on variant calling accuracy w/ and w/o the cleaning step? Here I'd like to distinguish QC and cleaning: while QC is just to read the data, ...
written 11 months ago by blueskypie50
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fastq reads cleaning
... In the [best practice for short variant discovery][1] from DNA sequencing, there is no mention of reads cleaning (removing adapters, low quality and short reads, etc.) . I wonder whether it's because such step is not necessary, or it's assumed the reads are already cleaned? If it's not necessary, i ...
reads fastq cleaning written 11 months ago by blueskypie50
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how to run GATK CalculateGenotypePosteriors on a case-control cohort
... One usage [example][1] is to refine genotypes based on the discovered allele frequency in an input VCF containing many samples ``` gatk CalculateGenotypePosteriors -V multisample_input.vcf.gz -O output.vcf.gz ``` Now if I have a case-control cohort of autoimmune disease, I wonder if I sho ...
gatk calculategenotypeposteriors written 11 months ago by blueskypie50
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variant calling with ALT contigs in hg38
... After reading the Board Institute tutorial on [variant calling with ALT contigs][1], just wonder if anyone can advise the scenario it is preferred over calling w/o ALT contigs? and any public study using variant calling with ALT contigs? Thanks! [1]: https://gatkforums.broadinstitute.org/gatk/d ...
next-gen written 13 months ago by blueskypie50 • updated 13 months ago by JC9.5k
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Answer: A: should I merge fastq files for different lanes before do QC?
... For RNAseq, I think whether merging lanes before or after mapping depends on your objective and the function of mapping program. For example, tophat may need all the reads to detect splice junction, i.e. lanes should be merged before mapping. But if the mapper maps each read independently, perhaps m ...
written 16 months ago by blueskypie50

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Popular Question 5.1 years ago, created a question with more than 1,000 views. For how to use bcftools isec to union two vcf files?

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