Mapping possition in SAM format

[leontovyc_roman]

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

[dpryan]

If the position is 6, then the first two bases were soft-clipped and the CIGAR string starts with 2S. You can, thus, parse the CIGAR string and modify the start position as appropriate. There are some functions in the pysam module that can help with this, should that be useful for you.

[leontovyc_roman]

If the position is 6, then the first two bases were soft-clipped and the CIGAR string starts with 2S. You can, thus, parse the CIGAR string and modify the start position as appropriate. There are some functions in the pysam module that can help with this, should that be useful for you.

Great, I piped couple of awk commands and it works perfectly. Thanks for saving my time

Roman