A solution would be to go through SAM, add the extra tag and convert back to
BAM:
samtools view -H old.bam > tmp.sam ; samtools view old.bam | awk '{printf
"%s\tOQ:Z:%s\n", $0, $11}' >> tmp.sam && samtools view -bo new.bam tmp.sam
From: Justin Jeyakani <[email protected]>
Sent: 20 April 2020 14:09
To: [email protected]
Subject: [Samtools-help] read and write a bam: but duplicate the quality column
(11) and write one with "OQ:Z:" flag [EXT]
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**
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