I am trying to extract specific columns from a .bam file. The columns are tagged with a prefix “TX:Z:” and “GX:Z:”. I seen people using perl to get specific columns, however, I don’t understand the logic well enough to adjust for my case. I can’t just save the output and subset in R because the file is too large.

Otherwise, if there is a samtools solution, that would also be great. I am trying to extra the accession numbers. The bam files were generated from scRNAseq libraries and cell ranger (10x).

Here are 3 lines:

A01604:525:HKHMKDRX3:2:2178:19253:32612                         16                  NC_030416.2              10591         255               47M2I41M                      *                     0                        0                        TGATAAATACACAGTTCATTCCTCATACACAAAGACAAAATAAAACACAGAGTATTACAGACGACAAAAGAGAAGGAAGATGGAGATGTG                        FFFFFFFFFFFFFFFF:FFFF,FFF:FFFFFF::FFFF:FFF:F:F:F:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF                       NH:i:1        HI:i:1                        AS:i:80       nM:i:0        RG:Z:SP1L_IGM_plus:0:1:HKHMKDRX3:2               TX:Z:XR_008397195.1,+3112,41M2I47M                    GX:Z:khdc4                        GN:Z:khdc4                 fx:Z:khdc4                      RE:A:E       xf:i:25         CR:Z:TTGACCCCCATCGTTG                       CY:Z:FFFFFFFFFFFFF:FF                        CB:Z:TTGACCCCAATCGTTG-1                   UR:Z:ACCCTAACCCCA              UY:Z:FFFFFFFFFFFF                       UB:Z:ACCCTAACCCCA
A01604:525:HKHMKDRX3:1:2144:31973:6167    16                  NC_030416.2              10800         255               90M             *                     0                     0                        ACAGACAACGATGCATCCAGATGTCTGTTAGGGAATTAAGAGTTTTAATATTATTTCTTGTAGCTTCCAAAGTCTTTACTCTGGCTGGTG                        FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF          NH:i:1        HI:i:1                        AS:i:84       nM:i:2        RG:Z:SP1L_IGM_plus:0:1:HKHMKDRX3:1               TX:Z:XR_008397195.1,+2901,90M            GX:Z:khdc4                        GN:Z:khdc4                 fx:Z:khdc4                      RE:A:E       xf:i:25         CR:Z:ACCTGAATCGCCAATA                        CY:Z:FFFFFFFFFFFFFFFF                        CB:Z:ACCTGAATCGCCAATA-1                   UR:Z:AGGGCACTGTCA            UY:Z:FFFFFFFFFFFF                       UB:Z:AGGGCACTGTCA
A01604:525:HKHMKDRX3:2:2163:18810:10958                         1040            NC_030416.2              10839         255               73M17S    *                     0                     0                        GAGTTTTAATATTATTTCTTGTAGCTTCCAAAGTCTTTACTCTGGCTGGTGTTATGAGGTAAAATAGGGGATTAGGTGTAAGTATTACAG                        FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF          NH:i:1        HI:i:1                        AS:i:69       nM:i:1        RG:Z:SP1L_IGM_plus:0:1:HKHMKDRX3:2               TX:Z:XR_008397195.1,+2879,17S73M                          GX:Z:khdc4                        GN:Z:khdc4                 fx:Z:khdc4                      RE:A:E       xf:i:17         CR:Z:ACCTGAATCGCCAATA                        CY:Z:FFFFFFFFFFFF:FFF                        CB:Z:ACCTGAATCGCCAATA-1                   UR:Z:AGGGCACTGTCA            UY:Z:FFFFFFFFFFFF                       UB:Z:AGGGCACTGTCA

I tried selecting the specific columns using awk but it seems like the in some rows there is an extra tab, meaning an extra column is added to these rows.