User: abascalfederico

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abascalfederico1.0k
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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 3 months ago by abascalfederico1.0k
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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 months ago by abascalfederico1.0k
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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 months ago by abascalfederico1.0k
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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 months ago by abascalfederico1.0k • updated 3 months ago by Devon Ryan79k
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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 7 months ago by abascalfederico1.0k • updated 7 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 10 months ago by abascalfederico1.0k
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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 10 months ago by abascalfederico1.0k • updated 10 months ago by trausch1.0k
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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 11 months ago by abascalfederico1.0k
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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 11 months ago by abascalfederico1.0k
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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 12 months ago by abascalfederico1.0k

Latest awards to abascalfederico

Popular Question 10 weeks ago, created a question with more than 1,000 views. For strange issues with absent EOF markers in BAM files
Guru 3 months ago, received more than 100 upvotes.
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 6 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 Duplicated read names in Fastq file
Popular Question 7 months ago, created a question with more than 1,000 views. For Duplicated read names in Fastq file
Popular Question 10 months ago, created a question with more than 1,000 views. For List of CNV (copy number variation) regions in the human genome
Student 11 months ago, asked a question with at least 3 up-votes. For Samtools' mpileup with pysam: enabling and disabling BAQ probabilistic realignment
Commentator 12 months 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 12 months ago, created a question with more than 1,000 views. For List of CNV (copy number variation) regions in the human genome
Popular Question 14 months ago, created a question with more than 1,000 views. For F3 test for admixture
Commentator 15 months ago, created a comment with at least 3 up-votes. For C: Is it good practice to convert lowewst quality genotyes to missing?
Scholar 16 months ago, created an answer that has been accepted. For A: How to properly merge multiple runs into one bam file ?
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: distance between two genes
Scholar 19 months ago, created an answer that has been accepted. For A: How to properly merge multiple runs into one bam file ?
Student 19 months ago, asked a question with at least 3 up-votes. For Samtools' mpileup with pysam: enabling and disabling BAQ probabilistic realignment
Scholar 19 months ago, created an answer that has been accepted. For A: How to properly merge multiple runs into one bam file ?
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Commentator 2.2 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 2.2 years ago, created an answer that has been accepted. For A: How to properly merge multiple runs into one bam file ?
Scholar 2.2 years ago, created an answer that has been accepted. For A: How to properly merge multiple runs into one bam file ?
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: distance between two genes
Scholar 2.3 years ago, created an answer that has been accepted. For A: How to properly merge multiple runs into one bam file ?
Scholar 2.3 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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