User: William

gravatar for William
William4.0k
Reputation:
4,030
Status:
Trusted
Location:
Europe
Last seen:
3 weeks, 4 days ago
Joined:
5 years, 7 months ago
Email:
w*****@hubrecht.eu

about me

Posts by William

<prev • 299 results • page 1 of 30 • next >
0
votes
2
answers
222
views
2
answers
Comment: C: How to display a VCF/BCF file or stream as a paginated table in a python web fra
... Thanks I will have a look. Is thinks the correct link for xbrowse? https://github.com/macarthur-lab/seqr/tree/master/xbrowse ? It's wat google gives me and it is part of something called seqr. Do you have any additional documentation about xbrowse? And which stack is too slow for 100 samples? ...
written 7 weeks ago by William4.0k
0
votes
2
answers
222
views
2
answers
Comment: C: How to display a VCF/BCF file or stream as a paginated table in a python web fra
... I was thinking to use cyvcf2 to read the first 500 variants at the start of the file or the first 500 in a region of interest https://github.com/brentp/cyvcf2 . cyvcf2 can use the vcf.gz or bcf.csi index. From the cyvcf2 variant records I can create a simple table that I am looking to display using ...
written 7 weeks ago by William4.0k
3
votes
2
answers
222
views
2
answers
How to display a VCF/BCF file or stream as a paginated table in a python web framework (e.g. Django)?
... Does anyone know how display a VCF/BCF file or stream as a paginated table in a python web framework (e.g. Django)? Is this possible at all? The number of variants (i.e records) can be kept low trough pagination (e.g. 500). Number of samples (i.e. columns) might be several 100. I was thinki ...
vcf gui written 7 weeks ago by William4.0k
0
votes
2
answers
241
views
2
answers
How to do a local denovo assembly including unmapped paired reads for many samples to genotype a large insertion.
... I have a set of many bam files for which I would like to know if an insertion of a few 100bp is present at a certain locus. The insertion variant is not picked up by small variant callers like freebayes, gatk or structural variant callers like lumpy or manta when doing a full genome variant callin ...
local assembly written 3 months ago by William4.0k • updated 3 months ago by h.mon9.7k
0
votes
1
answer
255
views
1
answers
Comment: C: Is it possible to use haplotypes instead of SNPs for association testing with ph
... Thank you for the haplotype association link. I'll look in to the tools / papers listed there. I added a reference for what I mean with genomic selection as a comment to the orginal question. ...
written 4 months ago by William4.0k
0
votes
1
answer
255
views
1
answers
Comment: C: Is it possible to use haplotypes instead of SNPs for association testing with ph
... Reference for genomic selection method http://www.genetics.org/content/157/4/1819 ...
written 4 months ago by William4.0k
2
votes
1
answer
255
views
1
answer
Is it possible to use haplotypes instead of SNPs for association testing with phenotypes?
... > We need to start thinking about genome analysis as haplotype reconstruction- not variant calling https://twitter.com/deannachurch/status/877192436459745280 Using new technology like linked reads or long reads it is becoming much easier to identify haplotypes in genomes, ie. collections of phas ...
haplotypes gwas snp written 4 months ago by William4.0k • updated 4 months ago by GabrielMontenegro330
0
votes
0
answers
250
views
0
answers
Comment: C: Python library for parsing bcftools stats file
... pyvcf is parsing VCF files, I am looking for a parser for VCF/BCF **stats** files generated by **bcftools stats**. ...
written 4 months ago by William4.0k
0
votes
0
answers
250
views
0
answers
Python library for parsing bcftools stats file
... Did someone already create a python library for parsing bcftools stats output files? BCFTools stats generates a txt stats file from VCF/BCF files. These text stats files contains some tab delimited tables and key value pairs that I would like to acces programmatically in python. Depending on the ...
bcftools written 4 months ago by William4.0k
1
vote
2
answers
308
views
2
answers
Answer: A: How to determine percentage missing genotypes in VCF/BCF?
... I always prefer not having to write custom code, but this is short and will do the trick: from cyvcf2 import VCF reader = VCF("my.vcf.gz") num_var = 0 num_called = 0 for variant in reader: num_var += 1 num_called += variant.num_called num_called / (num_var ...
written 5 months ago by William4.0k

Latest awards to William

Student 7 weeks ago, asked a question with at least 3 up-votes. For Difference Between Somatic And Germline Variant Calling?
Student 10 weeks ago, asked a question with at least 3 up-votes. For Difference Between Somatic And Germline Variant Calling?
Student 5 months ago, asked a question with at least 3 up-votes. For Recent Review / Best practices for (meta) micro array expression data analysis
Popular Question 5 months ago, created a question with more than 1,000 views. For Best Fastq Quality Overview Tool
Good Question 7 months ago, asked a question that was upvoted at least 5 times. For Best Genome Browser To Look At Structural Variation Calls

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1027 users visited in the last hour