The problem
This is related to another issue I recently opened, as this one complements the other.
The issue is that when running samtools import -i with Illumina data, some data get lost. Nowadays the Illumina data that contain UMIs have the following shape:
@<instrument>:<run number>:<flowcell_ID>:<lane>:<tile>:<x_pos>:<y_pos>:<umi> <read>:<is_filtered>:<control_number>:<index_sequence>
@LH00000:10:22WWW2LT4:1:1101:12488:1084:CCAATGTGC 1:N:0:TACGCTAC+CGTGTGAT
When running samtools import -i (explicitly using the -i flag to parse Illumina data), almost all information gets processed except for the UMI, which remains at the ID. But the natural place for the UMI in a SAM file is at the RX tag, and chances are that you will need some downstream process to move that UMI to that location, while the natural place where to perform that reorganization is samtools import.
Performing this move downstream prevents a subsequent samtools fastq from recovering all the information (UMI missing): that's what the related issue tries to cover.
The solution
I'd like samtools import -i to parse the ID to extract the UMI and store it in a tag (RX by default, as directed by the standard, or on a user defined tag).
The problem
This is related to another issue I recently opened, as this one complements the other.
The issue is that when running
samtools import -iwith Illumina data, some data get lost. Nowadays the Illumina data that contain UMIs have the following shape:When running
samtools import -i(explicitly using the-iflag to parse Illumina data), almost all information gets processed except for the UMI, which remains at the ID. But the natural place for the UMI in a SAM file is at the RX tag, and chances are that you will need some downstream process to move that UMI to that location, while the natural place where to perform that reorganization issamtools import.Performing this move downstream prevents a subsequent
samtools fastqfrom recovering all the information (UMI missing): that's what the related issue tries to cover.The solution
I'd like
samtools import -ito parse the ID to extract the UMI and store it in a tag (RX by default, as directed by the standard, or on a user defined tag).