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I've been looking for SNPs that have a few no-calls out of
about 20 for reliable ones. I also looked at indels and
found none.
But for SNPs I did find several under L176.1 and YP326 =
6777158 G > C .
What is odd is that the vast majority of no-calls
in these, which are
22228615 G>T
22269858 C>G
22270062 T>C
22270127 C>T
22271724 G>T
22271726 C>T
are, when looked at in the bam files, apparently
perfectly good calls. There are a few cases
where there are numbers of ancestral/derived
like 20/80 or 6/20 that are thus iffy. The "read quality"
shown by Bamview is quite OK.
A striking example is 22228615G>T . ALL
of one person’s bam reads (22 of them) are T!
Yet there is a one-position gap there in the bed file.
And here the real quality is all top-notch. And
there's no sign of misalignment. And it fits phylogenetically.
Does anybody have any idea what's going on?
I've written Mittelman about this and hopefully his
lab people will know.
Doug McDonald
about 20 for reliable ones. I also looked at indels and
found none.
But for SNPs I did find several under L176.1 and YP326 =
6777158 G > C .
What is odd is that the vast majority of no-calls
in these, which are
22228615 G>T
22269858 C>G
22270062 T>C
22270127 C>T
22271724 G>T
22271726 C>T
are, when looked at in the bam files, apparently
perfectly good calls. There are a few cases
where there are numbers of ancestral/derived
like 20/80 or 6/20 that are thus iffy. The "read quality"
shown by Bamview is quite OK.
A striking example is 22228615G>T . ALL
of one person’s bam reads (22 of them) are T!
Yet there is a one-position gap there in the bed file.
And here the real quality is all top-notch. And
there's no sign of misalignment. And it fits phylogenetically.
Does anybody have any idea what's going on?
I've written Mittelman about this and hopefully his
lab people will know.
Doug McDonald
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