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Old 02-01-2012, 03:28 AM   #1
evonne16
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hi,
There s error message ,when I use GATK. Please give me some advice,thanks

ERROR MESSAGE: SAM/BAM file SAMFileReader{/home/evonne/work/exome_data/result/GATA1_3_1.sorted.bam} is malformed: Read HWI-ST1106:141:C09YVACXX:3:1308:12485:83335 is either missing the read group or its read group is not defined in the BAM header
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Old 02-01-2012, 05:57 AM   #2
dpryan
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You can use picard tools to add the read group information to reads lacking a read group.
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Old 02-01-2012, 06:26 AM   #3
evonne16
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thanks,but i am a freshman,so how will i know what information of read group is i need?
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Old 02-01-2012, 07:13 AM   #4
dpryan
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Well, the information in the read group describes the sample, the platform used to sequence it, as well as a library identifier. You should be able to ask your grad student/post-doc/PI (or whomever you're directly working under) what he or she would like listed there.

The utility of read groups becomes more apparent with some downstream analyses, particularly if multiple files are merged together. For example, if you need to remove reads which are PCR duplicates, it's nice to have a designation of which library individual reads belong to. GATK can make use of some of the read group information to structure it's analyses, which makes life easier for us users!
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Old 02-01-2012, 04:47 PM   #5
evonne16
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thanks so much for your help!
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