User: abascalfederico

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abascalfederico1.1k
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Posts by abascalfederico

<prev • 177 results • page 1 of 18 • next >
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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 16 months 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 16 months 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 16 months 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 16 months ago by abascalfederico1.1k • updated 16 months ago by Devon Ryan90k
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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 20 months ago by abascalfederico1.1k • updated 20 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 23 months 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 23 months ago by abascalfederico1.1k • updated 5 months ago by pammybiotech0
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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 24 months ago by abascalfederico1.1k
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Why ExAC used bwa aln instead of mem?
... Anyone knows why in ExAC they used bwa `aln` instead of `mem`? I am not sure of the read lengths but somewhere said something about 150 bps x 2. Does it make sense to use bwa aln here? I though for long reads mem was the best choice The actual parameters used in ExAC were: bwa aln q 5 -l 32 -k ...
exac bwa written 24 months ago by abascalfederico1.1k
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Comment: C: Tool To Generate Venn Diagrams for 8 data sets?
... I know they are popular but Venn diagrams with more than 3 sets are very hard to read!! Why not just a matrix (table) with the numbers for all sets intersections, diagonals having the size of the sets? Or if you want to some graph rather than a table, why not a multidimensionality reduction strategy ...
written 2.1 years ago by abascalfederico1.1k

Latest awards to abascalfederico

Popular Question 4 months ago, created a question with more than 1,000 views. For strange issues with absent EOF markers in BAM files
Popular Question 7 months ago, created a question with more than 1,000 views. For strange issues with absent EOF markers in BAM files
Popular Question 8 months ago, created a question with more than 1,000 views. For strange issues with absent EOF markers in BAM files
Popular Question 8 months ago, created a question with more than 1,000 views. For samtools mpileup: position of each base within their reads
Popular Question 10 months ago, created a question with more than 1,000 views. For strange issues with absent EOF markers in BAM files
Popular Question 15 months ago, created a question with more than 1,000 views. For strange issues with absent EOF markers in BAM files
Guru 16 months ago, received more than 100 upvotes.
Popular Question 17 months ago, created a question with more than 1,000 views. For strange issues with absent EOF markers in BAM files
Popular Question 19 months ago, created a question with more than 1,000 views. For strange issues with absent EOF markers in BAM files
Popular Question 19 months ago, created a question with more than 1,000 views. For Duplicated read names in Fastq file
Popular Question 20 months ago, created a question with more than 1,000 views. For Duplicated read names in Fastq file
Popular Question 23 months ago, created a question with more than 1,000 views. For List of CNV (copy number variation) regions in the human genome
Student 24 months ago, asked a question with at least 3 up-votes. For Samtools' mpileup with pysam: enabling and disabling BAQ probabilistic realignment
Commentator 2.1 years ago, created a comment with at least 3 up-votes. For C: Is it good practice to convert lowewst quality genotyes to missing?
Popular Question 2.1 years ago, created a question with more than 1,000 views. For List of CNV (copy number variation) regions in the human genome
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Commentator 2.3 years ago, created a comment with at least 3 up-votes. For C: Is it good practice to convert lowewst quality genotyes to missing?
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Scholar 2.7 years ago, created an answer that has been accepted. For A: How to properly merge multiple runs into one bam file ?
Student 2.7 years ago, asked a question with at least 3 up-votes. For Samtools' mpileup with pysam: enabling and disabling BAQ probabilistic realignment
Scholar 2.7 years ago, created an answer that has been accepted. For A: How to properly merge multiple runs into one bam file ?
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