User: evolozzy

gravatar for evolozzy
evolozzy40
Reputation:
40
Status:
New User
Location:
University of Pennsylvania
Website:
https://evolozzy.net/
Twitter:
evolozzy
Last seen:
15 minutes ago
Joined:
1 year, 10 months ago
Email:
o**********@protonmail.com

Posts by evolozzy

<prev • 17 results • page 1 of 2 • next >
0
votes
0
answers
141
views
0
answers
Comment: C: how to extract cleaned SNPs from the main genotype data after QC?
... Can you clarify your question? 1. What is the file format? GEN, VCF, BED etc are all genotype data files. 2. What exactly do you need? The positions of SNPs or something else. ...
written 16 days ago by evolozzy40
0
votes
1
answer
175
views
1
answers
Comment: C: Filtering multi-allelic sites in VCF files
... Can you explain why? The filtering step can be different for different people, in my case I have 5 samples, and I am excluding the if an alternative allele is lower than 2 in any sample and the count of it is lower than 5 in all samples. Also the rest of my filtering is not included here. ...
written 19 days ago by evolozzy40
0
votes
1
answer
175
views
1
answers
Comment: C: Filtering multi-allelic sites in VCF files
... That's correct, but depends on the application! I use this for poolseq. So I really don't care about the genotypes. All I need is the allele frequencies. And for my data, I'm pretty confident that those are sequencing errors. I already remove anything below 5%. This was another step to do it. ...
written 20 days ago by evolozzy40
1
vote
1
answer
175
views
1
answers
Answer: A: Filtering multi-allelic sites in VCF files
... Found the answer! 1. Convert multiallelic to biallelic vcf first bcftools norm -m - file.vcf > biallellic.vcf 2. Filter the alternative alleles under certain value bcftools view -e "FORMAT/AD[:1]<2 && INFO/AD[1]<5" biallelic.vcf > biallelic-filtered.vc ...
written 20 days ago by evolozzy40
0
votes
1
answer
175
views
1
answers
Comment: C: Filtering multi-allelic sites in VCF files
... I tried but both `bcftools` and `vcffilter`, they put a cutoff value, then exclude the site all together, I want to keep the site and get rid of the extra allele. This is for poolseq analysis, that's why the read depths matter. ...
written 4 weeks ago by evolozzy40
0
votes
2
answers
307
views
2
answers
Comment: C: How to create a sequence alignment graph?
... If the gaps are aligned too, (which means all your alignments have the same length) it would work. ...
written 4 weeks ago by evolozzy40
2
votes
2
answers
307
views
2
answers
Answer: A: How to create a sequence alignment graph?
... You can use `geom_tile` in R by assigning values to Reference and Alternate alleles (0 and 1 would work) Then plot it position on x axis and the alignment on Y axis. The rest is aesthetic settings. ...
written 5 weeks ago by evolozzy40
3
votes
1
answer
175
views
5 follow
1
answer
Filtering multi-allelic sites in VCF files
... I am trying to filter multi-allelic sites in a VCF file to find the true multi allelic sites. Some of these have 1 read in 200, that I want to get rid of. The other alternative looks good. However, when I try to filter the alleles lower than frequency (0.05) with `vcftools` it gets rid of all varian ...
vcf multiallelic sites variant caliing snp written 5 weeks ago by evolozzy40
0
votes
0
answers
95
views
0
answers
Comment: C: What is the input to Plink's distance matrix function?
... What do you mean by concatenated VCF? If you've called the variants from multiple samples in a single vcf file i.e. every sample is a column after the INFO columns, that should be enough. If not you need to use `bcftools merge` to merge your vcf files. ...
written 5 weeks ago by evolozzy40
0
votes
2
answers
166
views
2
answers
Comment: C: How to create a SNP VCF file?
... Do you need specifically the SNPs? ...
written 6 weeks ago by evolozzy40

Latest awards to evolozzy

Scholar 20 days ago, created an answer that has been accepted. For A: R: poppr: Problems converting vcf to genclone object
Scholar 21 days ago, created an answer that has been accepted. For A: R: poppr: Problems converting vcf to genclone object
Scholar 6 months ago, created an answer that has been accepted. For A: R: poppr: Problems converting vcf to genclone object

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2662 users visited in the last hour
_