Moderator: Jorge Amigo

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Jorge Amigo11k
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Location:
Santiago de Compostela, Spain
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https://www.researchga...
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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

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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 5 days 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 27 days 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 7 weeks 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 while (<>) { chomp unless /^>/; print } and run it perl script.pl out.fasta ...
written 8 weeks 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 5 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 6 months ago by Jorge Amigo11k
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Answer: A: filtering a VCF file based on genotype
... from your question I understand that you have 1 single vcf file with 2 samples (germline and tumor) in it, and that you want to filter out all variants where 1 or the 2 samples have an empty genotype (./.) if this is the case, a simple `grep` should be enough: grep -vP '\t\./\.' file.vcf > ...
written 8 months ago by Jorge Amigo11k
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Comment: C: Is indel realigning necessary for INDEL discovery?
... I must agree with you both. I've updated my answer to be more precise on what GATK states and how I personally have always considered it. thank you for the clarification. ...
written 9 months ago by Jorge Amigo11k
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Answer: A: Is indel realigning necessary for INDEL discovery?
... GATK's HaplotypeCaller is both capable of detecting SNVs and InDels using a method that performs local *de novo* assembly (kind of a local realignment) to call variants, although it doesn't output any realigned bam. so, in summary, there's no need to use IndelRealigner if you are going to call varia ...
written 9 months ago by Jorge Amigo11k
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Answer: A: find positions of a short sequence in a genome
... here are my 2 cents for a one-liner perl solution to look for a particular motif in a genome (change the `$seqMotif` variable to look for your motif of interest; note that it accepts a `regex` pattern) that prints the positions where the motif happens to appear: time perl -ne 'BEGIN { $seqM ...
written 13 months ago by Jorge Amigo11k

Latest awards to Jorge Amigo

Epic Question 28 days ago, created a question with more than 10,000 views. For How To Split A .Vcf.Gz File
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Which Version Of Gatk Do People Use
Great Question 7 weeks ago, created a question with more than 5,000 views. For Which Programs Are You Relying On For Solid Data Analysis?
Good Answer 8 weeks 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 8 weeks 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 10 weeks ago, created an answer with at least 3 up-votes. For A: Which Version Of Gatk Do People Use
Good Answer 12 weeks 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 3 months ago, created a post with more than 5 votes. For A: Order Of Gatk Commands
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: How To Analyse Snp Data From Different Sources?
Scholar 5 months ago, created an answer that has been accepted. For A: Filtration of bam file but with header
Great Question 5 months ago, created a question with more than 5,000 views. For LinkedIn PubMed Importer
Appreciated 5 months ago, created a post with more than 5 votes. For A: Order Of Gatk Commands
Teacher 5 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
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Which Version Of Gatk Do People Use
Scholar 6 months ago, created an answer that has been accepted. For A: Filtration of bam file but with header
Good Answer 6 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 6 months ago, created a post with more than 5 votes. For A: Order Of Gatk Commands
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Which Version Of Gatk Do People Use
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?
Good Answer 9 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 9 months ago, created a post with more than 5 votes. For A: Order Of Gatk Commands
Appreciated 9 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
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Which Version Of Gatk Do People Use

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