Moderator: Jorge Amigo

gravatar for Jorge Amigo
Jorge Amigo11k
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Location:
Santiago de Compostela, Spain
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https://www.researchga...
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Last seen:
1 day, 11 hours ago
Joined:
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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 • 758 results • page 1 of 76 • next >
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Comment: C: Multiline Fasta To Single Line Fasta
... thanks for pointing it out. I've corrected my previous answer and tested thoroughly the new one. ...
written 1 day ago by Jorge Amigo11k
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Comment: C: how to remove multiallelic from VCF
... note that the merging process when normalizing can be quite intense on such large files as gnomad's, so if you are interested in particular regions do not forget to indicate this in your normalization command. I've edited my answer to reflect this. ...
written 5 weeks ago by Jorge Amigo11k
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Comment: C: how to remove multiallelic from VCF
... I have always used vcf.gz, although I've seen vcf.bgz probably to indicate that the compression has been performed with the `bgzip` algorithm rather than simply `gzip`. but this is simply informative for the human user, not for the software. ...
written 5 weeks ago by Jorge Amigo11k
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Comment: C: how to remove multiallelic from VCF
... [bcftools' documentation][1] is very clear about this > Use -m2 -M2 -v snps to only view biallelic SNPs. so if it isn't working it must be either a problem with `bcftools` (that'd be odd) or either a problem with gnomad data. if you query gnomad data for that particular position you'll see th ...
written 6 weeks ago by Jorge Amigo11k
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Comment: C: Merge hundreds bedgraph files with unionbedg in one bash line
... that's precisely what `-header` option does. the above command `bedtools unionbedg -i *.bedgraph -filler NA -header` does exactly what you need. ...
written 9 weeks ago by Jorge Amigo11k
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Comment: C: bwa mem on a bam file
... from [bwa manual page][1]: > If -p is used, the command assumes the 2i-th and the (2i+1)-th read in reads.fq constitute a read pair (such input file is said to be interleaved) but unfortunately `samtools fastq` does not output interleaved reads. you can either try sorting reads by name BEFORE ...
written 12 weeks ago by Jorge Amigo11k
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Comment: C: Remove a list of positions form a VCF file
... my answer was very simple. this one adds more *grep* functionality: `-F` option looks for fixed strings rather than regular expressions, and `-w` option looks for whole words rather than just matching patterns. I don't know how `-F` works in conjunction with `-w`, but it looks like an overall faster ...
written 3 months ago by Jorge Amigo11k
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Comment: C: Multiline Fasta To Single Line Fasta
... just create a simple script.pl file containing this (do not use!) while (<>) { chomp unless /^>/; print } EDIT: the previous code is wrong. use this one into script.pl instead: while (<>) { $. > 1 and /^>/ ? print "\n" : chomp; print } and run it perl script.pl ...
written 3 months ago by Jorge Amigo11k
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Answer: A: Identifying private and shared SNPs using VCFtools
... update: *bcftools isec* does exactly these kind of comparisons, and faster. this quick example bcftools isec -p isec_results file1 file2 generates in a *isec_results* folder vcf files with private variants from *file1*, private variants from *file2*, *file1* variants shared with *file2*, and * ...
written 7 months ago by Jorge Amigo11k
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Answer: A: h38 total genes ?
... locate refGene file, uncompress it, look for the 13th column containing gene names, make sure there are no repetitions, and count them: curl http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/refGene.txt.gz \ | zcat | cut -f13 | sort -u | wc -l 28054 ...
written 8 months ago by Jorge Amigo11k

Latest awards to Jorge Amigo

Good Answer 27 days 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?
Scholar 28 days ago, created an answer that has been accepted. For A: Filtration of bam file but with header
Appreciated 28 days ago, created a post with more than 5 votes. For A: Order Of Gatk Commands
Epic Question 3 months ago, created a question with more than 10,000 views. For How To Split A .Vcf.Gz File
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Which Version Of Gatk Do People Use
Great Question 3 months ago, created a question with more than 5,000 views. For Which Programs Are You Relying On For Solid Data Analysis?
Good Answer 3 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?
Good Answer 4 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?
Teacher 4 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
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: How To Analyse Snp Data From Different Sources?
Scholar 7 months ago, created an answer that has been accepted. For A: Filtration of bam file but with header
Great Question 7 months ago, created a question with more than 5,000 views. For LinkedIn PubMed Importer
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 8 months ago, created an answer with at least 3 up-votes. For A: Which Version Of Gatk Do People Use
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Which Version Of Gatk Do People Use
Scholar 8 months ago, created an answer that has been accepted. For A: Filtration of bam file but with header
Good Answer 8 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 8 months ago, created a post with more than 5 votes. For A: Order Of Gatk Commands
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Which Version Of Gatk Do People Use
Good Answer 10 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?
Good Answer 11 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 11 months ago, created a post with more than 5 votes. For A: Order Of Gatk Commands

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