Moderator: Jorge Amigo

gravatar for Jorge Amigo
Jorge Amigo12k
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12,150
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Location:
Santiago de Compostela, Spain
Website:
https://www.researchga...
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Google Scholar Page
Last seen:
18 hours ago
Joined:
10 years, 9 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

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Comment: C: how to combine two bed files using the same ID information
... ... and the simplest I would go for. Considering that `join` output provides the ID in the first column, here's a minimum modification to exactly match the desired output: join -t $'\t' -1 4 -2 4 <(sort -k4,4 file1.bed) <(sort -k4,4 file2.bed) | perl -pe 's/(\S+)\t(.+)/$2\t$1/' ...
written 9 weeks ago by Jorge Amigo12k
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Answer: A: how to combine two bed files using the same ID information
... perl -lane '$d{$F[3]} .= "@F[0..2] "; END { foreach $i (keys %d) { print $d{$i}.$i } }' file1.bed file2.bed | awk '$5~/./' ...
written 9 weeks ago by Jorge Amigo12k
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Answer: A: Is there a tool to predict if a missense variant causes a loss of function on th
... https://pcingola.github.io/SnpEff/se_inputoutput/#loss-of-function-lof-and-nonsense-mediated-decay-nmd-predictions ...
written 9 weeks ago by Jorge Amigo12k
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Answer: A: Heterozygous types in VCF
... The reference allele is an arbitrary nomenclature which the VCF format must use, therefore the only important thing for your model should be the alleles found at each particular position of the genome. ...
written 9 weeks ago by Jorge Amigo12k
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Comment: C: Filter VCF with bash commands
... A simpler yet general solution would be this one: perl -ne 'print if /QD=([-\d.]+)/ and $1>8' file.vcf If you don't want to lose the headers in the filtering process, then you should go for this one: perl -ne 'print if /^#/ or (/QD=([-\d.]+)/ and $1>8)' file.vcf Although I definite ...
written 11 weeks ago by Jorge Amigo12k
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Comment: C: Failed to open plain.vcf: unknown file type
... The error you're seeing is due to the content of that tag on a particular line, so if you find the offending line you'll be able to trace the error. The definition of the GP tag in the header seems fine, although I'm not used to that tag and it could be a problem if you define it as `integer` while ...
written 12 weeks ago by Jorge Amigo12k
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Answer: A: Failed to open plain.vcf: unknown file type
... Your first `sed` substitutes the first `fileformat` line for the `FORMAT` one. Your sed 's/^##fileformat=VCFv4.1/##FORMAT=/' should be instead sed 's/^##fileformat=VCFv4.1/##fileformat=VCFv4.1\n##FORMAT=/' or even better this one in order to see your change at the bottom of the header ...
written 12 weeks ago by Jorge Amigo12k
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Answer: A: How to create a SNP VCF file?
... The VCF extension may be used for vCard files, but in the context of SNPs and genotyping, a minimum google search should have taken you to [The Variant Call Format Specification][1] [1]: https://samtools.github.io/hts-specs/VCFv4.3.pdf ...
written 12 weeks ago by Jorge Amigo12k
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Comment: C: How to count the number of alignments in a bam file without using samtools?
... Just a couple of comments: `-u` implies `-b`, therefore `samtools view -u input.bam` is enough to get an uncompressed bam file. Also, if you only need to know the number of reads, generating all flagstat metrics is not that efficient, and `samtools view -c input.bam` would be sufficient. It won't ...
written 12 weeks ago by Jorge Amigo12k
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Comment: C: How to count the number of alignments in a bam file without using samtools?
... Even if uncompressed, which is recommended for piping purposes in order to save time compressing and decompressing output and input respectively, a bam file is still binary, so `wc -l` will not work. ...
written 12 weeks ago by Jorge Amigo12k

Latest awards to Jorge Amigo

Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Which Version Of Gatk Do People Use
Scholar 8 weeks ago, created an answer that has been accepted. For A: Check if REF allele is minor allele in any variant
Scholar 3 months ago, created an answer that has been accepted. For A: Check if REF allele is minor allele in any variant
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Which Version Of Gatk Do People Use
Scholar 3 months ago, created an answer that has been accepted. For A: Check if REF allele is minor allele in any variant
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?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Which Version Of Gatk Do People Use
Appreciated 3 months ago, created a post with more than 5 votes. For A: Order Of Gatk Commands
Scholar 3 months ago, created an answer that has been accepted. For A: Check if REF allele is minor allele in any variant
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Which Version Of Gatk Do People Use
Scholar 4 months ago, created an answer that has been accepted. For A: Check if REF allele is minor allele in any variant
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Which Version Of Gatk Do People Use
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: How To Analyse Snp Data From Different Sources?
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 8 months ago, created a post with more than 5 votes. For A: Order Of Gatk Commands
Commentator 12 months ago, created a comment with at least 3 up-votes. For C: How To Analyse Snp Data From Different Sources?
Good Answer 12 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 14 months ago, created an answer that has been accepted. For A: Filtration of bam file but with header
Good Answer 14 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 14 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 15 months ago, created a post with more than 5 votes. For A: Order Of Gatk Commands
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Which Version Of Gatk Do People Use
Scholar 15 months ago, created an answer that has been accepted. For A: Filtration of bam file but with header

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