Moderator: Jorge Amigo

gravatar for Jorge Amigo
Jorge Amigo10k
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Santiago de Compostela, Spain
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https://www.researchga...
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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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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 29 days ago by Jorge Amigo10k
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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 9 weeks ago by Jorge Amigo10k
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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 3 months ago by Jorge Amigo10k
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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 3 months ago by Jorge Amigo10k
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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 8 months ago by Jorge Amigo10k
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Comment: C: Splitting A Vcf File
... thanks a lot for this idea. it is indeed much faster (3x at least on a local test splitting 3 exomes), and it can be condensed as follows: bcftools query -l MyData.vcf.gz | parallel -a - \ bcftools view -c1 -s {} -Oz --threads 8 -o {}.vcf.gz MyData.vcf.gz ...
written 8 months ago by Jorge Amigo10k
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Comment: C: How To Split Multiple Samples In Vcf File Generated By Gatk?
... sure. since you will be generating a file per sample you could just simply use `-o $sample.vcf.gz`, but I personally prefer to keep the original file name to know where that data came from. for that reason I use `.o ${file/.vcf*/.$sample.vcf.gz}`, which uses a bash string manipulation function to su ...
written 9 months ago by Jorge Amigo10k
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Comment: C: Tools To Calculate Average Coverage For A Bam File?
... that's because `NR` is an `awk` variable that stores the number of rows, therefore the `c` variable on my code is not wrong, but it is superfluous. ...
written 9 months ago by Jorge Amigo10k
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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 10 months ago by Jorge Amigo10k
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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 months ago by Jorge Amigo10k

Latest awards to Jorge Amigo

Teacher 29 days ago, created an answer with at least 3 up-votes. For A: Which Version Of Gatk Do People Use
Scholar 29 days ago, created an answer that has been accepted. For A: Filtration of bam file but with header
Good Answer 29 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?
Appreciated 29 days ago, created a post with more than 5 votes. For A: Order Of Gatk Commands
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?
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?
Appreciated 3 months ago, created a post with more than 5 votes. For A: Order Of Gatk Commands
Appreciated 4 months ago, created a post with more than 5 votes. For A: Order Of Gatk Commands
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Which Version Of Gatk Do People Use
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Which Version Of Gatk Do People Use
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Which Version Of Gatk Do People Use
Appreciated 4 months ago, created a post with more than 5 votes. For A: Order Of Gatk Commands
Appreciated 5 months ago, created a post with more than 5 votes. For A: Order Of Gatk Commands
Appreciated 5 months ago, created a post with more than 5 votes. For A: Order Of Gatk Commands
Popular Question 6 months ago, created a question with more than 1,000 views. For force reads to map to a particular genome region
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
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?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Which Version Of Gatk Do People Use
Appreciated 8 months ago, created a post with more than 5 votes. For A: Order Of Gatk Commands
Good Answer 9 months ago, created an answer that was upvoted at least 5 times. For A: Phased And Unphased Genotypes In Vcf Files: Does The Order Of Alleles Matter?
Appreciated 9 months ago, created a post with more than 5 votes. For A: Order Of Gatk Commands
Great Question 10 months ago, created a question with more than 5,000 views. For LinkedIn PubMed Importer
Scholar 11 months ago, created an answer that has been accepted. For A: Filtration of bam file but with header

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