Hi all,
This is my first post here. Just searching this site has answered so many questions I've had previously, but I can't find an answer to this one. If I have hard trimmed some bases from the beginning of my reads after alignment, this leaves me with the possibility of a correctly-mapped deletion beginning a read. The SAM spec seems ambiguous to me on this topic, and if this is valid, which position should I take to be the leftmost mapped position? For example, say I hard trim the first three bases from the following aligned read:
reference: ACTGACGTCA
read: ACTCGTCA
CIGAR: 3M2D5M
This is now:
read: CGTCA
CIGAR 3H2D5M
There may not be a correct answer to this question, so maybe I'm just asking will SAMTOOLS pileup get confused by this?
Thanks!
Stuart
This is my first post here. Just searching this site has answered so many questions I've had previously, but I can't find an answer to this one. If I have hard trimmed some bases from the beginning of my reads after alignment, this leaves me with the possibility of a correctly-mapped deletion beginning a read. The SAM spec seems ambiguous to me on this topic, and if this is valid, which position should I take to be the leftmost mapped position? For example, say I hard trim the first three bases from the following aligned read:
reference: ACTGACGTCA
read: ACTCGTCA
CIGAR: 3M2D5M
This is now:
read: CGTCA
CIGAR 3H2D5M
There may not be a correct answer to this question, so maybe I'm just asking will SAMTOOLS pileup get confused by this?
Thanks!
Stuart
Comment