one question in GATK

evonne16 · 02-01-2012, 03:28 AM

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

dpryan · 02-01-2012, 05:57 AM

You can use picard tools to add the read group information to reads lacking a read group.

evonne16 · 02-01-2012, 06:26 AM

thanks,but i am a freshman,so how will i know what information of read group is i need?

dpryan · 02-01-2012, 07:13 AM

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!

evonne16 · 02-01-2012, 04:47 PM

thanks so much for your help！

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02-01-2012, 03:28 AM	#1
evonne16 Junior Member Location: shanghai Join Date: Nov 2011 Posts: 7	one question in GATK 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

02-01-2012, 05:57 AM	#2
dpryan Devon Ryan Location: Freiburg, Germany Join Date: Jul 2011 Posts: 3,480	You can use picard tools to add the read group information to reads lacking a read group.

02-01-2012, 06:26 AM	#3
evonne16 Junior Member Location: shanghai Join Date: Nov 2011 Posts: 7	thanks,but i am a freshman,so how will i know what information of read group is i need?

02-01-2012, 07:13 AM	#4
dpryan Devon Ryan Location: Freiburg, Germany Join Date: Jul 2011 Posts: 3,480	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!

02-01-2012, 04:47 PM	#5
evonne16 Junior Member Location: shanghai Join Date: Nov 2011 Posts: 7	thanks so much for your help！