read and write a bam: but duplicate the quality column (11) and write one with "OQ:Z:" flag

Question

[gnanakkan]

Hi All,

I have over 1000 bam files and I need to read and write them as bam files. The output bam shd contain a header with the alignment, but the column 11 (quality) to be repeated once, the second should contain quality with "OQ:Z:" flag. The script/package/tools shd be robust. Appreciated providing the script or tools to do this! Thanks in advance.

eg: input bam::

E00579:50:HK2VJALXX:6:1220:15300:41040  2115    chr1    9999    0       90H60M  chr5    18606598        0       GATAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC    JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJFJJJJFJJJJJFFJJJJJJJJJFJ<A    SA:Z:chr5,18606834,-,51S99M,37,0;     MD:Z:60 PG:Z:MarkDuplicates     RG:Z:HK2VJALXX.6        NM:i:0  AS:i:60 XS:i:58

E00579:50:HK2VJALXX:6:1212:4066:24884   113     chr1    9999    0       34S60M56S       chr5    18606897        0       CCTAGAACAGCTCTTCCTTTATTTTCTTTTTCTGGATAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACAGAGATAACTATTGATACAACACCTTCATGACCCTAAGGTACTATCATAGAGTTCT<<-FA-7<AFF<<<7<FJAF-JFJFF-J<JJAAJFFF-AAJJJJFJJJJJAJJJJJJFAJJJJJJJJFJJJJJJJJJJF<FJJJFJJJJFJJFJFJJJJJJJFJJJJJJJJJJFJJJJFJJJJJJJJFJJJJJJJJJJJJJJJJJFFFAA  SA:Z:chr5,18606769,+,58M92S,0,0;chr5,18606834,+,107S43M,0,0;    MD:Z:60 PG:Z:MarkDuplicates     RG:Z:HK2VJALXX.6   NM:i:0     AS:i:60 XS:i:59

output bam::

E00579:50:HK2VJALXX:6:1220:15300:41040  2115    chr1    9999    0       90H60M  chr5    18606598        0       GATAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC    JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJFJJJJFJJJJJFFJJJJJJJJJFJ<A    SA:Z:chr5,18606834,-,51S99M,37,0;     MD:Z:60 PG:Z:MarkDuplicates     RG:Z:HK2VJALXX.6        NM:i:0  AS:i:60 XS:i:58 OQ:Z:JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJFJJJJFJJJJJFFJJJJJJJJJFJ<A

E00579:50:HK2VJALXX:6:1212:4066:24884   113     chr1    9999    0       34S60M56S       chr5    18606897        0       CCTAGAACAGCTCTTCCTTTATTTTCTTTTTCTGGATAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACAGAGATAACTATTGATACAACACCTTCATGACCCTAAGGTACTATCATAGAGTTCT<<-FA-7<AFF<<<7<FJAF-JFJFF-J<JJAAJFFF-AAJJJJFJJJJJAJJJJJJFAJJJJJJJJFJJJJJJJJJJF<FJJJFJJJJFJJFJFJJJJJJJFJJJJJJJJJJFJJJJFJJJJJJJJFJJJJJJJJJJJJJJJJJFFFAA  SA:Z:chr5,18606769,+,58M92S,0,0;chr5,18606834,+,107S43M,0,0;    MD:Z:60 PG:Z:MarkDuplicates     RG:Z:HK2VJALXX.6   NM:i:0     AS:i:60 XS:i:59  OQ:Z:T<<-FA-7<AFF<<<7<FJAF-JFJFF-J<JJAAJFFF-AAJJJJFJJJJJAJJJJJJFAJJJJJJJJFJJJJJJJJJJF<FJJJFJJJJFJJFJFJJJJJJJFJJJJJJJJJJFJJJJFJJJJJJJJFJJJJJJJJJJJJJJJJJFFFAA

[GenoMax]

Since OQ:Z tags contain Q scores before calibration, I assume you are looking to do calibration of Q scores rather than just I have over 1000 bam files and I need to read and write them as bam files..

So perhaps GATK BaseRecalibrator followed by ApplyBQSR?