rsIds will be in the 4th and 5th columns, r^2 in the 7th column.
Details of the lossy compression scheme, for the record:
D' and r^2 values in the range of [0,1] are encoded like this:
encodedValue = 'a' + (actualValue * 9)
D' values in the range [-1,0) are encoded like th
ce is reverse-complemented if necessary to match the forward
strand of the target/reference. Thus the CIGAR string marches forward
through the query sequence and the reference/target sequence."
--
Brooke Rhead
UCSC Genome Bioinformatics Group
On 11/24/11 8:37 AM, Carsten Raabe wrote:
>
seeing:
>
> "This is a SAM/BAM quirk: the strand flag is only a historical note.
> The query sequence is reverse-complemented if necessary to match the
> forward strand of the target/reference. Thus the CIGAR string marches
> forward through the query sequence and the refere
