Hello all,
I used samtools pileup command with –c option. Based on the manual the consensus quality, SNP quality and RMS mapping quality of the reads covering the site are added as 3 columns. But I don’t quite understand how these qualities are defined. And what does RMS mapping quality means? I could not find relevant information anywhere.
Also the manual says that ‘An indel occupies an additional line. Each indel line consists of chromosome name, , the genotype, .., the first alllele, the second allele,..’ The problem is that I frequently see inconsistency between the genotype and the second allele, such as the line 1, 2 and 4 in the following chunk from the pileup file.
genotype first alllele second allele
+G/+G +G *
+G/+G +G *
*/+T * +T
*/+A * +A
*/* * +G
I would really appreciate any suggestions/comments.
Moreover, I had some problem with tview. I posted the problem in the sticky SAM thread, and lparsons reported the same problem next, but we got no response so far.
Here is my old post again:
I tried samtools tview to browse the alignment results in bam format. However, several keys do not work, including:
Arrows Small scroll movement
J, K Large scroll movement
backspace Scroll back one screen
..
I haven’t checked other keys. But would like to report what I saw. BTW, is there any other ways besides tview to view the alignment results in sam/bam format? Thanks a lot!
I used samtools pileup command with –c option. Based on the manual the consensus quality, SNP quality and RMS mapping quality of the reads covering the site are added as 3 columns. But I don’t quite understand how these qualities are defined. And what does RMS mapping quality means? I could not find relevant information anywhere.
Also the manual says that ‘An indel occupies an additional line. Each indel line consists of chromosome name, , the genotype, .., the first alllele, the second allele,..’ The problem is that I frequently see inconsistency between the genotype and the second allele, such as the line 1, 2 and 4 in the following chunk from the pileup file.
genotype first alllele second allele
+G/+G +G *
+G/+G +G *
*/+T * +T
*/+A * +A
*/* * +G
I would really appreciate any suggestions/comments.
Moreover, I had some problem with tview. I posted the problem in the sticky SAM thread, and lparsons reported the same problem next, but we got no response so far.
Here is my old post again:I tried samtools tview to browse the alignment results in bam format. However, several keys do not work, including:
Arrows Small scroll movement
J, K Large scroll movement
backspace Scroll back one screen
..
I haven’t checked other keys. But would like to report what I saw. BTW, is there any other ways besides tview to view the alignment results in sam/bam format? Thanks a lot!
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