I am looking to re-call a large number of legacy exomes which have been previously called (using different pipelines). To do this, I am following the Broad's best practices to revert a BAM to a uBAM: http://gatkforums.broadinstitute.org/firecloud/discussion/6484/
That process is making sense, but one question that came up while I was mucking about in the reads was that SM tag, which I understand to mean "Sample" was different on different reads of the same sample. For example, here are two reads from one sample (nuclotides redacted);
Read1:
H7FL7BBXX160404:2:2115:11809:26494 99 1 10004 18 3S60M1I9M3S = 10359 429 "sequence here" @>?>?@B@@B@@CAAB@@CAAB@@CAAB@@CAAB@@CAAB@@AAAB@@CAA?@@@AAB@@:AAB@@@;A>A>==@= MC:Z:2S74M MD:Z:69 PG:Z:MarkDuplicates.A RG:Z:H7FL7.2AM:i:18 NM:i:1 SM:i:18 MQ:i:18 OQ:Z:AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJFJJFJJJJJ7JJJJJJ<JFJJJJJF UQ:i:0
Read2:
H7FL7BBXX160404:2:1124:24282:45361 163 1 10005 15 27M1I48M = 10247 318 "sequence here" <:>>?@>>A@@=>>A@@@>>A@@@>>>@AA???B@@A??>AAA@@CAAB@?CAAB@@@AAB@@C1AA??9?>><=# MC:Z:76M MD:Z:3A5A5A5A6A10A35 PG:Z:MarkDuplicates.ARG:Z:H7FL7.2 AM:i:15 NM:i:7 SM:i:15 MQ:i:15 OQ:Z:AAFFFJJJJJJFJJJJJJJJJJJJJJFJJJJJJJJJJJJAJJJJJJJJJJJJJJJJJFJJJJJJ<JJJJ7JJJJJ# UQ:i:242
In the reads above, I do not understand why the first read has SM:i:18 while the second is SM:i:15 - aren't these from the same sample? Shouldn't they be the same? What am I missing here?
Thanks!
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danny.k.wells •
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I think you are confusing the SM tag that is part of the RG group with the SM tag that is part of the reads' tags. If you look at the header of the bam file you should see that each @RG entry has a SM tag that indicates that sample group. E.g.:
samtools view -H TCRBOA1-N-WEX.bam | grep '^@RG'
@RG ID:TCRBOA1-N-WEX.bam LB:TCRBOA1-N-WEX.bam PL:illumina SM:TCRBOA1-N-WEX.bam PU:NA
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That's not true: SM stands for "Template independant Mapping quality". https://github.com/samtools/hts-specs/blob/master/SAMtags.pdf
The friendlier URL is http://samtools.github.io/hts-specs/SAMtags.pdf — better to point people to that than to an URL containing details like branch names that may change in future.
branch names are cucks