Moderator: Jorge Amigo

gravatar for Jorge Amigo
Jorge Amigo11k
Reputation:
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Location:
Santiago de Compostela, Spain
Website:
https://www.researchga...
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Last seen:
4 days, 13 hours ago
Joined:
10 years, 2 months ago
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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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Answer: A: Comparing multiple columns from 2 files using awk, perl or python
... It doesn't exactly answer your question, but if you're dealing with regions you may want to have a look to `bedtools`: $ bedtools intersect -a file1.bed -b file2.bed -wa SpoScf_15890 12 2376 SpoScf_07684 10 4075 SpoScf_07684 64 4276 Super_scaffold_60 ...
written 8 weeks ago by Jorge Amigo11k
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Comment: C: How to count fastq reads
... the only very slight problem I see is that very rare 1 base sequences (trimmed perhaps) with "+" quality would be counted twice, but I love the simplicity of this answer. ...
written 4 months ago by Jorge Amigo11k
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Comment: C: Evaluate the sensitivity and specificity of vcf files
... although chr1 is one of the biggest ones, and considering that you've already done the largest effort which is calling variants on NA12878, I'd definitely go for the entire genome's numbers rather than being fine with a relatively small subset of statistics. ...
written 6 months ago by Jorge Amigo11k
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Answer: A: Evaluate the sensitivity and specificity of vcf files
... you've chosen a reference sample to apply your variant calling pipeline to. well done, because you're almost there. just get a set of [high confidence NA12878 variants][1] such as the [GiB project][2] ones, use a comparison tool such as [RTG vcfeval][3] (the one recommended by the [GiB project][4]), ...
written 6 months ago by Jorge Amigo11k
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Answer: A: vcftools separate only selected chrom allocation from 4gb vcf file
... it's difficult to say anything without knowing the content of your VCF file, but here are a couple of suggestions: 1. have you checked your VCF and your BED files refer to the same reference? one quick dirty check is making sure that you're either using or not using in both files the "chr" prefix, ...
written 6 months ago by Jorge Amigo11k
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Answer: A: BAM file and Bedgraph file don't match after bedtools genomecov?
... you should check if IGV is filtering any kind of reads. typically this is caused by IGV's default duplicate reads filtering. just unselect everything you see under "View > Preferences > Alignments > Filter..." and you should see in IGV's coverage track the same profile than the Bedgraph ha ...
written 6 months ago by Jorge Amigo11k
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Answer: A: How to use bcftools query -f to extract three alleles from multisample vcf file
... if you already have exome data from each parent, if you have aligned it, and you have called variants, then you would have already ended up with 2 bam files and 2 vcf files. if you need now to compare variants among them you don't have to map them again. you just have to compare the vcf files you a ...
written 8 months ago by Jorge Amigo11k
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Comment: C: Filter unique SNPs (rows) in VCF/text file
... sorting such a big file only for being able to use the uniq function wouldn't be the more efficient way to do it, plus a simple `sort -u` wouldn't address the problem described in the question as the lines that need to be merged/skipped do vary. if sorting would be considered (and it would be really ...
written 8 months ago by Jorge Amigo11k
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Comment: C: Filter unique SNPs (rows) in VCF/text file
... this is the same as an uniq function on entire lines, and it doesn't work with your example considering that positions qualities vary from line to line. you need to group (index) only the columns you expect to be repeated, as explained in the example I suggested previously. ...
written 8 months ago by Jorge Amigo11k
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Answer: A: Can I split a bed file into 1000bp bins and add up my read numbers?
... I don't know of a direct method to accomplish what you need, but have a look at this tentative proposal: awk 'FS=OFS="\t"{print $1, 0, $2}' human_hg19.fa.fai \ | bedtools makewindows -b - -w 1000 \ | bedtools map -a - -b input.bedgraph -c 4 -o sum \ | grep -P "\d$" what it does is: ...
written 8 months ago by Jorge Amigo11k

Latest awards to Jorge Amigo

Appreciated 6 weeks ago, created a post with more than 5 votes. For A: Order Of Gatk Commands
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: How To Analyse Snp Data From Different Sources?
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?
Good Answer 7 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 7 months ago, created an answer that has been accepted. For A: Filtration of bam file but with header
Good Answer 7 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
Scholar 8 months ago, created an answer that has been accepted. For A: Filtration of bam file but with header
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Which Version Of Gatk Do People Use
Scholar 9 months ago, created an answer that has been accepted. For A: Filtration of bam file but with header
Scholar 9 months ago, created an answer that has been accepted. For A: Filtration of bam file but with header
Epic Question 13 months ago, created a question with more than 10,000 views. For LinkedIn PubMed Importer
Popular Question 13 months ago, created a question with more than 1,000 views. For Which Programs Are You Relying On For Solid Data Analysis?
Appreciated 14 months ago, created a post with more than 5 votes. For A: Order Of Gatk Commands
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
Appreciated 16 months ago, created a post with more than 5 votes. For A: Order Of Gatk Commands
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Which Version Of Gatk Do People Use
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?
Scholar 17 months ago, created an answer that has been accepted. For A: Filtration of bam file but with header
Appreciated 17 months ago, created a post with more than 5 votes. For A: Order Of Gatk Commands
Epic Question 19 months ago, created a question with more than 10,000 views. For How To Split A .Vcf.Gz File
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Which Version Of Gatk Do People Use
Great Question 20 months ago, created a question with more than 5,000 views. For Which Programs Are You Relying On For Solid Data Analysis?
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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