Samtools tview help
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7.4 years ago
emth4657 ▴ 10

Hello,

I am having some trouble understanding my samtools tview output.

I have attached a screen shot of when I use the command:

samtools tview NODE_1202.sorted.bam NODE_1202.fa

https://s18.postimg.org/fywys3ytl/Screen_Shot_2016_11_18_at_3_07_08_PM.png

The other question I have is what do the R/M/S mean in the second line? I have attached an image of what I am talking about enter image description here

If these are my SNPs and Indels how do I remove them? I need a "clean" sequence without errors.

samtools tview snps indels • 6.8k views
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Entering edit mode
7.4 years ago

I am having some trouble understanding my samtools tview output.

press 'H' to get help. '.' is match on forward strand ',' is match on negative strand.

'R' to show the bases.

R/M/S mean in the second line

consensus with degenerate nucleotide alphabet https://en.wikipedia.org/wiki/Nucleic_acid_notation

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what do the red * indicate?

How do I remove errors/anomalies?

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I don't think you really want to remove errors or anomalies. What do you aim to achieve? This is probably not the way to go.

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7.4 years ago

R/M/S are standard IUPAC ambiguity codes that are shown if you have mismatches/variants at a site. Note that *** indicates an insertion. Underlined reads are either secondary alignments or orphans (hit ? and look at the bottom). If the reads are colored, then that indicates their MAPQ.

I have absolutely no idea what you want to achieve by removing indels or SNPs. Regarding errors, I suppose any difference that isn't called a variant could in theory be called an error and changed in the BAM file, but as a general rule that's a really bad idea. It's best to explain what your actual goal is.

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Remove was not the proper words, correct would be more appropriate.

I need to correct any snps or indels. I am not sure how to do that/how to tell if I have done that.

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What would correcting SNPs even mean? What is your goal?

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