User: yarmda

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yarmda0
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Posts by yarmda

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Comment: C: bedtools: extracting no coverage regions
... Hi Aaron, I just want to bump one of the replies to this comment. I would also like to summarize coverage by region. Is that doable with bedtools? > This has worked very well, thank you! > I am now looking to calculate average coverage for my CDS features, one value per CDS, and I can't see ...
written 10 weeks ago by yarmda0
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Comment: C: How best to parse samtools mpileup results?
... How does this work behind the scenes? I'm finding the order of the PL:DP:AD flags is reversed when the FILTER lists "PASS" compared to when it is "NOT_TARGET_ORGANISM_STRAIN" ...
written 10 weeks ago by yarmda0
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Comment: C: How best to parse samtools mpileup results?
... This has been exceedingly helpful. Now, if I wanted to print the AD and the DP instead of the INFO column and instead of filtering on the AD - would that be possible? ...
written 10 weeks ago by yarmda0
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Comment: C: How best to parse samtools mpileup results?
... I tried that to no success. Below I define the variable allele to be T, the same as the original expression. I have replaced "T" in getDisplayString().equals("T") with "$allele", but now everything is considered false. Have I made a mistake? allele="T" echo $allele java -jar dist/vcffi ...
written 10 weeks ago by yarmda0
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Comment: C: How best to parse samtools mpileup results?
... Can you describe how to pass a shell variable to the javascript expression? ...
written 10 weeks ago by yarmda0
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Comment: C: How best to parse samtools mpileup results?
... That's good thinking. I considered the loop, but hadn't realized how I could avoid loading the entire vcf each iteration. ...
written 10 weeks ago by yarmda0
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Comment: C: How best to parse samtools mpileup results?
... This looks really close to what I want. Is there a way I can feed the expression a file containing a series of positions with alleles of interest and a minimum AD? ...
written 10 weeks ago by yarmda0
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Comment: C: How best to parse samtools mpileup results?
... That doesn't look too much different from the pileup output. The greater difficulty I'm having isn't parsing out the AD feature, but doing so when comparing the alternate allele value at that point. It would be straightforward to write an if statement of the kind: if ALT column is T then retur ...
written 10 weeks ago by yarmda0
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How best to parse samtools mpileup results?
... I am trying to characterize the depth of coverage for SNPs/INDELs/other variants in my BAM/SAM file. Using samtools mpileup generates a nice VCF that gives me information on this, but it's not quite complete. Entering the "-t AD" flag gives me the depth of the alternate alleles compared to the refer ...
vcf samtools vcftools mpileup written 11 weeks ago by yarmda0 • updated 10 weeks ago by Pierre Lindenbaum91k
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Comment: C: Variant calling - display nucleotides with 0 coverage
... Thanks for showing me this, Brian. I understand the risks of calling variants in these regions. I downloaded your code and ran it as you listed. I'm only seeing variants here, not regions of the genome where my reads aligned perfectly. Is there another setting for this? I don't see such an option ...
written 3 months ago by yarmda0

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