Hi all,
I have question concerning the SAM format. I need to define position of read mapped to the reference. Which means position of first base of the read regardless if matched or not to reference. I know there is field POS in SAM format but it refers to position of the first matched base.
example:
reference-AGCATGTTAGATAAGTGTCTAGGATCATATGCATGA
mapped read--TAGTTAGATAAGTGT
using this example POS is 6 - the first matched base is G on the 6th position of the reference
however I need to get 4 because T is the aligned with 4th position
Do you have any idea how to get this information from SAM format?
cheers
Roman
I have question concerning the SAM format. I need to define position of read mapped to the reference. Which means position of first base of the read regardless if matched or not to reference. I know there is field POS in SAM format but it refers to position of the first matched base.
example:
reference-AGCATGTTAGATAAGTGTCTAGGATCATATGCATGA
mapped read--TAGTTAGATAAGTGT
using this example POS is 6 - the first matched base is G on the 6th position of the reference
however I need to get 4 because T is the aligned with 4th position
Do you have any idea how to get this information from SAM format?
cheers
Roman
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