User: Nina
Nina • 340
- Reputation:
- 340
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- New User
- Location:
- Vancouver, BC, Canada
- Last seen:
- 7 years, 8 months ago
- Joined:
- 9 years ago
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Posts by Nina
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... fwiw, I marked this reply as helpful because the @PG tags are optional, and you give some good suggestions of what to look for if the info is not in the bam header. ...
written 8.1 years ago by
Nina • 340
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Answer:
A: Samtools Mpileup Output
... The symbols "<" and ">" were added to column 5 a few releases ago. These symbols mean that this position is "covered" by a large gap (ie we're inside the "N" element in the cigar of this read). Note that reads that have a gap at this position still contribute to the total coverage reported in ...
written 8.4 years ago by
Nina • 340
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... Generally snp callers work in two passes, where the first pass identifies every position with at least one mismatching base, and the second pass filters these results to generate the list of snps you think are "real".
I get the sense that you have only done the first pass.
You need to decide how t ...
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... I would argue that no, you cannot (reliably) analyze anything that aligns outside the targeted regions in exon capture data. If you see a dense region of coverage outside a targeted region, one of two things has happened:
a) the reads really came from there and they were capture due to off-target bi ...
written 8.5 years ago by
Nina • 340
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Comment:
C: Help Understanding Pileup Format
... If you run "samtools pileup" with no other parameters, you will get a usage message with a full list of the param options and their default settings.
You will see that the bitwise filtering is set with "-m INT" option (it will exclude reads with bits in INT)
In version 0.1.14 the default value for t ...
written 8.6 years ago by
Nina • 340
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Comment:
C: Help Understanding Pileup Format
... Sorry I mixed up the -c and -v options in my answer.
(-v means only report variants, -c means identify potential snps)
As you have probably figured out, the samtools pileup file can have several formats depending on the options used to create it. If your pileup file really looks like the example you ...
written 8.6 years ago by
Nina • 340
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... First things first: samtools will call the variants for you, if you include the -v option when generating the pileup. There is also a script called varFilter which will sift through the pileup and only report snps that it believes are likely to be real.
see http://samtools.sourceforge.net/cns0.sht ...
written 8.6 years ago by
Nina • 340
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Answer:
A: Genotypes For Snps
... I think you're not getting any answers because the question is very unclear.
Unless I'm missing something, the only way to determine the genotype is to look at what is reported in the "Tumor_Seq_Allele1" and "Tumor_Seq_Allele2" columns of your MAF file.
Having said this, I'm confused as to why you h ...
written 8.7 years ago by
Nina • 340
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... Not only is the bed format 0-based, it's also "half-open", meaning the start position is inclusive, but the end position is not.
So if your region starts at position 100 and ends at 101 using standard 1-based coordinates with both start and end inclusive (ie it's two bases long), when you convert i ...
written 8.7 years ago by
Nina • 340
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... If you want to do some googling, the QC metric used by Illumina is called the "chastity filter". Chastity is a measure of the signal to noise ratio and is defined as the "the ratio of the highest of the four (base type) intensities to the sum of highest two."
The chastity threshold is 0.6 and this ...
written 8.8 years ago by
Nina • 340
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