User: abascalfederico

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abascalfederico1.1k
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Posts by abascalfederico

<prev • 179 results • page 1 of 18 • next >
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Answer: A: Extract samples with alternative genotype from a multi-sample VCF
... If you just want those lines with a "1" in the third column, you can add an awk command: bcftools view -r REGION OF INTEREST | filter_vep -filter 'IMPACT is MODERATE or IMPACT is HIGH' | filter_vep -filter MAX_AF <0.01 or not MAX_AF'' | bcftools view -i 'GT="alt"' | bcftools query -f "'[%CH ...
written 3 months ago by abascalfederico1.1k
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VCF human-chimp divergence?
... Anyone knows of a VCF containing all human-chimp divergent sites mapped on human genome coordinates? It would be so nice if this was available :-) Thanks! Federico ...
vcf written 17 months ago by abascalfederico1.1k
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Comment: C: How to get a list of reads supporting a variant in R?
... For a given position, I want to read the pileup and when there is a match to the variant, I want to get the mapping coordinates of the read matching the variant. I do not have the exact code yet, but it would imply something like: for pileupcolumn in samfile.pileup(chr,int(pos)-1,int(pos)): ...
written 3.1 years ago by abascalfederico1.1k
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Comment: C: How to get a list of reads supporting a variant in R?
... Thanks, Devon. I don't want the programmatic burden ;-) I will instead make a call to python from R - not what I wanted though ...
written 3.1 years ago by abascalfederico1.1k
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Comment: C: How to get a list of reads supporting a variant in R?
... Thanks Devon, I already had a look at that function, but it just provide a table of counts. I need to identify which reads support a given variant. This is relatively easy with pysam but I find no way to do this in Rsamtools. Maybe I missed something from the documentation? ...
written 3.1 years ago by abascalfederico1.1k
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How to get a list of reads supporting a variant in R?
... For a given position, in which there is a variant called by some algorithm, I want to get the pileup and analyse the reads supporting that variant. Any idea on how to do this in R? I know how to do this in Python using pysam but I need an R implementation. Thanks! ...
R bam written 3.1 years ago by abascalfederico1.1k • updated 3.1 years ago by Devon Ryan98k
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Tool to segment genome according to SNP density?
... Can anyone recommend a tool to segment the genome according to SNP density (using HMM-based segmentation, for example)? Thanks! ...
hmm snp density segmentation written 3.4 years ago by abascalfederico1.1k • updated 16 months ago by Biostar ♦♦ 20
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Comment: C: Program to calculate and add the NM tag to a bam file
... That's exactly what I needed, thanks! ...
written 3.6 years ago by abascalfederico1.1k
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Program to calculate and add the NM tag to a bam file
... Does anybody know of a program to add the NM tag (number of mismatches) to a BAM file? Usually aligned BAM files come with that tag, but I've found one without it and need that information. Thanks! ...
nm bam written 3.6 years ago by abascalfederico1.1k • updated 10 weeks ago by Biostar ♦♦ 20
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Comment: C: Why ExAC used bwa aln instead of mem?
... I'll send them an email, thanks for the suggestion. Regarding the use of bwa aln, I found it in the supplementary material of: Lek, M., Karczewski, K. J., Minikel, E. V., Samocha, K. E., Banks, E., Fennell, T., ... & Tukiainen, T. (2016). Analysis of protein-coding genetic variation in 60,706 hu ...
written 3.7 years ago by abascalfederico1.1k

Latest awards to abascalfederico

Popular Question 9 weeks ago, created a question with more than 1,000 views. For Recode VCF file according to ancestral alleles (AA)
Great Question 6 months ago, created a question with more than 5,000 views. For bedtools intersect bed and vcf, coordinates problem
Popular Question 6 months ago, created a question with more than 1,000 views. For BioPython, PhyloXML and duplication nodes
Popular Question 9 months ago, created a question with more than 1,000 views. For BioPython, PhyloXML and duplication nodes
Popular Question 10 months ago, created a question with more than 1,000 views. For BioPython, PhyloXML and duplication nodes
Popular Question 10 months ago, created a question with more than 1,000 views. For BioPython, PhyloXML and duplication nodes
Scholar 14 months ago, created an answer that has been accepted. For A: 23andMe SNP data does not correlate with UCSC. What am I doing wrong?
Popular Question 15 months ago, created a question with more than 1,000 views. For BioPython, PhyloXML and duplication nodes
Scholar 15 months ago, created an answer that has been accepted. For A: How to properly merge multiple runs into one bam file ?
Voter 17 months ago, voted more than 100 times.
Good Answer 20 months ago, created an answer that was upvoted at least 5 times. For A: samtools view - F 4 removes sam header and truncates file??
Appreciated 22 months ago, created a post with more than 5 votes. For A: samtools view - F 4 removes sam header and truncates file??
Popular Question 22 months ago, created a question with more than 1,000 views. For Uniquely mapped PAIRS of reads
Popular Question 22 months ago, created a question with more than 1,000 views. For samtools mpileup: position of each base within their reads
Popular Question 22 months ago, created a question with more than 1,000 views. For Recode VCF file according to ancestral alleles (AA)
Popular Question 2.1 years ago, created a question with more than 1,000 views. For strange issues with absent EOF markers in BAM files
Popular Question 2.3 years ago, created a question with more than 1,000 views. For strange issues with absent EOF markers in BAM files
Popular Question 2.4 years ago, created a question with more than 1,000 views. For strange issues with absent EOF markers in BAM files
Popular Question 2.4 years ago, created a question with more than 1,000 views. For samtools mpileup: position of each base within their reads
Popular Question 2.5 years ago, created a question with more than 1,000 views. For strange issues with absent EOF markers in BAM files
Popular Question 3.0 years ago, created a question with more than 1,000 views. For strange issues with absent EOF markers in BAM files
Guru 3.0 years ago, received more than 100 upvotes.
Popular Question 3.1 years ago, created a question with more than 1,000 views. For strange issues with absent EOF markers in BAM files
Popular Question 3.3 years ago, created a question with more than 1,000 views. For strange issues with absent EOF markers in BAM files
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Duplicated read names in Fastq file

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