User: Jautis

gravatar for Jautis
Jautis290
Reputation:
290
Status:
Trusted
Location:
United States
Last seen:
1 month ago
Joined:
5 years, 5 months ago
Email:
t***@duke.edu

Posts by Jautis

<prev • 104 results • page 1 of 11 • next >
0
votes
0
answers
537
views
0
answers
Comment: C: Phasing non-human genomes with Beagle - do I need to divide subjects by populati
... Did you find the answer to this? I'm looking for the same bit of information ...
written 4 weeks ago by Jautis290
0
votes
3
answers
5.9k
views
3
answers
Comment: C: How to remove a list of reads from fastq file?
... Hello, I'm trying this but (i) the quality score information isn't be returned and (ii) the '@' from the read name line is missing. Looking at the script, I can't figure out why this would be -- think you can help update it again? ...
written 7 weeks ago by Jautis290
0
votes
0
answers
160
views
0
answers
find position of snps in cM, given recombination map from ldhelmet
... Hello, I have a recombination map calculated from LDhelmet which has estimates of recombination rates for windows of the genome (in recombination events per generation per bp) and a separate file of SNP locations which I would like to transform from base number to location in centiMorgans. Is there ...
genome recombination physical position written 5 months ago by Jautis290
0
votes
0
answers
143
views
0
answers
Convert VCF + LDhelmet Recombination Rates to EIGENSTRAT format
... Hello, I have a vcf file of called variants (GATK) and genotypes per individual and a text file produced from LDhelmet which contains recombination rates for windows across the genome (4 columns: chromosome, start, end, and recombination rate). I'm looking to convert this to [the eigenstrat format]( ...
vcf linkage snp genome written 5 months ago by Jautis290
0
votes
1
answer
161
views
1
answers
Comment: C: sed (or similar) command to remove part of the FORMAT from a vcf file?
... Awesome, thank you! I didn't know bcf would get rid of tags in addition to writing new ones ...
written 5 months ago by Jautis290
2
votes
1
answer
161
views
1
answer
sed (or similar) command to remove part of the FORMAT from a vcf file?
... Hello, I'm looking for a quick way to remove PGT, PID, and PS from the FORMAT of a vcf file output by GATK. Currently, some sites have these flags while others don't (see example below). For downstream processing in another program, I need all sites to have the same flags and phasing information doe ...
vcf processing sed written 5 months ago by Jautis290 • updated 5 months ago by finswimmer13k
0
votes
1
answer
4.9k
views
1
answers
Comment: C: How to combine chromosome vcf files
... Hi Pierre, do you know if it's possible to use GatherVCFs with a list of files rather than a separate `I=` for each? Thanks! ...
written 5 months ago by Jautis290
0
votes
0
answers
325
views
0
answers
Comment: C: vcftools minDP filter not working for samtools genotype calling output
... Thanks! I was not aware of that. ...
written 9 months ago by Jautis290
1
vote
0
answers
325
views
0
answers
vcftools minDP filter not working for samtools genotype calling output
... Hello, I've called genotypes using samtools/bcftools and am now trying to filter the genotype calls based on mean depth (DP > 10). However, when I use the `minDP` filter in vcftools nothing happens. Alternately, the `minQ` filter seems to be working well. Any ideas why this is or what I could do? ...
genotype filtering snp snp-calling written 9 months ago by Jautis290
0
votes
1
answer
183
views
1
answer
Efficiently run blat for long sequences
... Hello, I'm using blat to align genes from one genome to another. This is working well for small sequences (<10kb), but longer sequences are running for an more than a day with no signs of finishing. This seems to be especially true for those 35kb+ and some of the sequences are near 200kb. Does ...
assembly sequence alignment blat written 11 months ago by Jautis290 • updated 10 months ago by Vitis2.4k

Latest awards to Jautis

Popular Question 3 months ago, created a question with more than 1,000 views. For Compare tree topologies (Newick)
Centurion 5 months ago, created 100 posts.
Popular Question 5 months ago, created a question with more than 1,000 views. For Compare tree topologies (Newick)
Popular Question 9 months ago, created a question with more than 1,000 views. For Compare tree topologies (Newick)
Popular Question 13 months ago, created a question with more than 1,000 views. For Compare tree topologies (Newick)
Popular Question 17 months ago, created a question with more than 1,000 views. For Compare tree topologies (Newick)
Popular Question 18 months ago, created a question with more than 1,000 views. For Compare tree topologies (Newick)
Popular Question 20 months ago, created a question with more than 1,000 views. For Compare tree topologies (Newick)
Popular Question 21 months ago, created a question with more than 1,000 views. For Compare tree topologies (Newick)
Popular Question 23 months ago, created a question with more than 1,000 views. For Compare tree topologies (Newick)
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Compare tree topologies (Newick)
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Compare tree topologies (Newick)
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Compare tree topologies (Newick)
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Taking genotypes out of a vcf file
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Help simulating RRBS reads
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Compare tree topologies (Newick)
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Compare tree topologies (Newick)
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Calling SNPs from RRBS data
Popular Question 3.3 years ago, created a question with more than 1,000 views. For Comparing two phylogenies
Popular Question 3.8 years ago, created a question with more than 1,000 views. For Modifying fasta file based on vcf information
Student 4.9 years ago, asked a question with at least 3 up-votes. For Comparing two phylogenies
Scholar 5.1 years ago, created an answer that has been accepted. For A: SNPs, genotypes, HWE in GWAS,
Teacher 5.1 years ago, created an answer with at least 3 up-votes. For A: Calculating the bisulfite conversion rate
Scholar 5.2 years ago, created an answer that has been accepted. For A: SNPs, genotypes, HWE in GWAS,

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1423 users visited in the last hour