User: blueskypie

gravatar for blueskypie
blueskypie40
Reputation:
40
Status:
New User
Location:
United States
Last seen:
3 weeks, 3 days ago
Joined:
4 years, 6 months ago
Email:
j*******@gmail.com

Posts by blueskypie

<prev • 13 results • page 1 of 2 • next >
0
votes
1
answer
108
views
1
answer
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 4 weeks ago by blueskypie40 • updated 4 weeks ago by chrchang5235.4k
0
votes
2
answers
108
views
2
answers
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 7 weeks ago by blueskypie40
0
votes
2
answers
108
views
2
answers
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 7 weeks ago by blueskypie40
0
votes
1
answer
184
views
1
answers
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 4 months ago by blueskypie40
0
votes
1
answer
184
views
1
answers
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 4 months ago by blueskypie40
0
votes
1
answer
184
views
1
answers
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 4 months ago by blueskypie40
0
votes
1
answer
184
views
1
answer
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 4 months ago by blueskypie40
0
votes
0
answers
139
views
0
answers
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 4 months ago by blueskypie40
0
votes
1
answer
286
views
1
answer
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 5 months ago by blueskypie40 • updated 5 months ago by JC8.0k
2
votes
2
answers
5.7k
views
2
answers
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 9 months ago by blueskypie40

Latest awards to blueskypie

Popular Question 4.5 years ago, created a question with more than 1,000 views. For how to use bcftools isec to union two vcf files?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1719 users visited in the last hour