Moderator: Jorge Amigo

gravatar for Jorge Amigo
Jorge Amigo12k
Reputation:
11,760
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Location:
Santiago de Compostela, Spain
Website:
https://www.researchga...
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Google Scholar Page
Last seen:
4 hours ago
Joined:
10 years, 5 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.

Posts by Jorge Amigo

<prev • 802 results • page 1 of 81 • next >
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Comment: C: Merge coordinates by gene ID
... I really like the rationale behind using the 4th column as chromosome and keeping the chromosome as mapping information with `-c` option. I love finding different ways of using tools that were designed to do a particular job in order to achieve a different goal. ...
written 2 days ago by Jorge Amigo12k
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Answer: A: Extract specific variant genome ID from a VCF file
... From [bcftools' documentation][1]: bcftools view -s HG00479 -o HG00479.chr9.vcf ftp:/­/­ftp.­1000genomes.­ebi.­ac.­uk/­vol1/­ftp/­data_collections/­1000_genomes_project/­release/­20190312_biallelic_SNV_and_INDEL/­ALL.­chr9.­shapeit2_integrated_snvindels_v2a_27022019.­GRCh38.­phased.­vcf.­gz No ...
written 7 days ago by Jorge Amigo12k
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Answer: A: Having some regex problems capturing strings with special chars. Could use some
... I can think of simplifying the regex a little bit using perl, in case it helps: perl -pe 's/\^\[\[(2J|3J|H|[01](;3[237])?m)//g; s/\^H//g; s/\|\/-//' run.log > run_clean.log ...
written 12 days ago by Jorge Amigo12k
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Answer: A: How to multiply all columns of a .csv table with a constant extracted from anoth
... Assuming both read_count.csv and all genefamilies.csv are tabulated files containing 2 columns (read_count.csv doesn't really matter), and that ´awk´ number formatting is enough for you: for file in *.genefamilies.csv; do awk -v m=$(grep -F -w ${file/.genefamilies.csv} read_count.csv | awk ...
written 19 days ago by Jorge Amigo12k
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Comment: C: How To Split Multiple Samples In Vcf File Generated By Gatk?
... Without knowing what exactly have you done, I'll assume that you have copied the second piece of code of my answer into `splitvcf.pl` and ran it to split all 1000g samples, and you're seeing that error you describe. If that's the case, you've done one thing right and one thing wrong: the right thing ...
written 26 days ago by Jorge Amigo12k
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Comment: C: Splitting A Vcf File
... If `ALLsamples.vcf` is a well formed multisample file, and is previously `bgzip` compressed, `tabix -p vcf ALLsamples.vcf.gz` should index it without complaining at all. Unfortunately if that doesn't work for you you'll have to find it out yourself, as you're facing a local issue. Some ideas: is tab ...
written 27 days ago by Jorge Amigo12k
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Comment: C: Splitting A Vcf File
... Share the command you used with us, so that we don't have to guess it. ...
written 27 days ago by Jorge Amigo12k
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Comment: C: How do I count a number of ("-") in a reference string and remove it in a secon
... This is not a Python solution, but Perl, and it's meant to be run in a unix/linux command line. Also, the sequences.fa file is expected to have unix EOL, so if that's not the case you may have to preprocess it with dos2unix or mac2unix. Also, this solution addresses exactly what your question was a ...
written 28 days ago by Jorge Amigo12k
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Answer: A: How do I count a number of ("-") in a reference string and remove it in a secon
... If a perl solution can be considered, here are my 2 cents: perl -pe 'if (/^>/) { $. > 1 and print "\n" } else { chomp }' sequences.fa \ | perl -pe '/^(-*)\w+(-*)$/ and printf "%s %s\n", length($1), length($2)' The first perl section linearizes the fasta file, and the second perl sect ...
written 29 days ago by Jorge Amigo12k
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Comment: C: Linearize fasta files
... Wow, what a nice comparison. Unfortunately I must say that my perl suggestion doesn't work as expected: $ time (perl -pe 'chomp unless /^>/' < Homo_sapiens.GRCh38.dna.primary_assembly.fa > /dev/null) does indeed join each header to the end of the previous sequence. This very slightly ...
written 29 days ago by Jorge Amigo12k

Latest awards to Jorge Amigo

Teacher 7 days ago, created an answer with at least 3 up-votes. For A: Which Version Of Gatk Do People Use
Scholar 7 days ago, created an answer that has been accepted. For A: Check if REF allele is minor allele in any variant
Commentator 4 weeks ago, created a comment with at least 3 up-votes. For C: How To Analyse Snp Data From Different Sources?
Appreciated 5 weeks ago, created a post with more than 5 votes. For A: Order Of Gatk Commands
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Which Version Of Gatk Do People Use
Teacher 11 weeks 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
Commentator 8 months ago, created a comment with at least 3 up-votes. For C: How To Analyse Snp Data From Different Sources?
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 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?
Scholar 10 months ago, created an answer that has been accepted. For A: Filtration of bam file but with header
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?
Appreciated 11 months ago, created a post with more than 5 votes. For A: Order Of Gatk Commands
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Which Version Of Gatk Do People Use
Scholar 11 months ago, created an answer that has been accepted. For A: Filtration of bam file but with header
Scholar 12 months ago, created an answer that has been accepted. For A: Filtration of bam file but with header
Scholar 12 months ago, created an answer that has been accepted. For A: Filtration of bam file but with header
Epic Question 15 months ago, created a question with more than 10,000 views. For LinkedIn PubMed Importer
Popular Question 15 months ago, created a question with more than 1,000 views. For Which Programs Are You Relying On For Solid Data Analysis?
Appreciated 16 months ago, created a post with more than 5 votes. For A: Order Of Gatk Commands
Good Answer 17 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 17 months ago, created a post with more than 5 votes. For A: Order Of Gatk Commands
Appreciated 19 months ago, created a post with more than 5 votes. For A: Order Of Gatk Commands
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Which Version Of Gatk Do People Use
Good Answer 20 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?

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