Moderator: Jorge Amigo

gravatar for Jorge Amigo
Jorge Amigo9.8k
Reputation:
9,810
Status:
Trusted
Location:
Santiago de Compostela, Spain
Website:
https://www.researchga...
Scholar ID:
Google Scholar Page
Last seen:
4 hours ago
Joined:
7 years, 3 months ago
Email:
a****@yahoo.com

Scrutinizing genomic human variation by dealing with high throughput genotyping and next generation sequencing results, among many other things.

Bioinformatician @ Genomic Medicine Group

Hospital Clínico Universitario, Santiago de Compostela, Spain

Posts by Jorge Amigo

<prev • 742 results • page 1 of 75 • next >
0
votes
1
answer
3.3k
views
1
answers
Comment: C: Filter Bam File Based On Coverage
... first, you have to detect those low coverage regions. then, you have to filter your bam file with those regions. I would suggest you open a new question rather than commenting a previous related one. ...
written 16 days ago by Jorge Amigo9.8k
0
votes
11
answers
106k
views
11
answers
Comment: C: Tools To Calculate Average Coverage For A Bam File?
... in addition, if you have already plotted depths it means that you have got a temporal R data.frame (or similar type) in there containing chromosome, position and depth information. splitting such data.frame by chromosome and calculating average values should be straight-forward. I would just suggest ...
written 12 weeks ago by Jorge Amigo9.8k
0
votes
0
answers
261
views
0
answers
Comment: C: RNA-SeQC gatkFlags option reading first word only
... it seems to be a problem with my `java` calling script. I also use aliases for `java7` and `java8`, although I didn't include them in the original question. it works fine when calling java directly and not through the aliases, so I'll have to correct my aliases for the future. thanks anyway ;) by t ...
written 4 months ago by Jorge Amigo9.8k
0
votes
0
answers
261
views
0
answers
Comment: C: RNA-SeQC gatkFlags option reading first word only
... I tried both escaping and not escaping the quotes with no success. I even found out that the `gatkFlags` option even accepts a string (well, a single word) even without being quoted. but nothing gets recognized after the first word. ...
written 4 months ago by Jorge Amigo9.8k
0
votes
0
answers
261
views
0
answers
Comment: C: RNA-SeQC gatkFlags reading first word only
... I've run it both from a script and manually, both with single and double quotation marks, both using a variable $THREADS and a fixed value. no success. I've edited the second example, since it was a copy-paste problem. I first tried using the large '--num_threads' option and then I also tried the ...
written 4 months ago by Jorge Amigo9.8k
1
vote
0
answers
261
views
0
answers
RNA-SeQC gatkFlags option reading first word only
... I have this issue: when I try to test `RNA-SeQC` using GATK's multi-threading I'm not seeing the entire `gatkFlags` string being read: java -jar $HOME/ngs/software/RNA-SeQC_v1.1.8.jar \ -strictMode \ -o $RNASEQC_FOLDER \ -r $REFERENCE_FASTA \ -t $REFERENCE_TRANSCRIPTOMIC \ - ...
gatkflags rna-seq rna-seqc written 4 months ago by Jorge Amigo9.8k
0
votes
3
answers
3.0k
views
3
answers
Comment: C: Split a VCF file into individual sample files
... you're right. I didn't realize the `-m 1` option that stops reading the file after the first match. ...
written 5 months ago by Jorge Amigo9.8k
0
votes
2
answers
462
views
2
answers
Comment: C: Extract vcf from 1000 genomes based on population and region
... in case you need to perform this 2-step process, it'd be much faster first to filter by region and then to select the samples. anyway, you can merge both commands in one: bcftools view -r 3:38589548-38691164 -S list_of_Punjabi_persons.txt -o PJL_SCN5A.vcf 1000_genomes_chr3.vcf ...
written 5 months ago by Jorge Amigo9.8k
2
votes
4
answers
1.3k
views
4
answers
Answer: A: Individual VCF files from main VCF file
... already stated [here][1] and [here][2]: for file in *.vcf*; do for sample in `bcftools query -l $file`; do bcftools view -c1 -Oz -s $sample -o ${file/.vcf*/.$sample.vcf.gz} $file done done [1]: https://www.biostars.org/p/78929/#115693 [2]: https://www.biostars.org/ ...
written 6 months ago by Jorge Amigo9.8k
0
votes
5
answers
848
views
5
answers
Answer: A: Splitting vcf files to individual samples
... already stated [here][1] and [here][2]: for file in *.vcf*; do for sample in `bcftools query -l $file`; do bcftools view -c1 -Oz -s $sample -o ${file/.vcf*/.$sample.vcf.gz} $file done done [1]: https://www.biostars.org/p/78929/#115693 [2]: https://www.biostars.org/ ...
written 6 months ago by Jorge Amigo9.8k

Latest awards to Jorge Amigo

Great Question 14 days ago, created a question with more than 5,000 views. For LinkedIn PubMed Importer
Scholar 4 weeks ago, created an answer that has been accepted. For A: Filtration of bam file but with header
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: Which Version Of Gatk Do People Use
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: Moore'S Law
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: Which Version Of Gatk Do People Use
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Which Version Of Gatk Do People Use
Appreciated 11 weeks ago, created a post with more than 5 votes. For A: Order Of Gatk Commands
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Which Version Of Gatk Do People Use
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: Building Vcftools Executable
Popular Question 4 months ago, created a question with more than 1,000 views. For Which Programs Are You Relying On For Solid Data Analysis?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Which Version Of Gatk Do People Use
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Which Version Of Gatk Do People Use
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: Is It Ok To Use One End Of A Set Of Paired-End Reads As A Set Of Single Reads?
Appreciated 5 months ago, created a post with more than 5 votes. For A: Order Of Gatk Commands
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Which Version Of Gatk Do People Use
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Which Version Of Gatk Do People Use
Appreciated 7 months ago, created a post with more than 5 votes. For A: Order Of Gatk Commands
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Which Version Of Gatk Do People Use
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Which Version Of Gatk Do People Use
Scholar 7 months ago, created an answer that has been accepted. For A: Filtration of bam file but with header
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Which Version Of Gatk Do People Use
Cylon 9 months ago, received 1,000 up votes.
Appreciated 9 months ago, created a post with more than 5 votes. For A: Order Of Gatk Commands
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: How To Analyse Snp Data From Different Sources?
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Which Version Of Gatk Do People Use

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1413 users visited in the last hour