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Old 02-14-2012, 04:20 AM   #1
Location: london, uk

Join Date: Nov 2010
Posts: 4
Default casava 1.8 bam conversion to gatk bam

Am am trying to convert bam files generated via casava to bam files recognized by gatk...I have asked illumina but no solution yet. I am using casava 1.8 to align and generate bam files(one bam file for all chr's). Illumina gave me a script which was supposed to work for conversion, but as far as I can see produces the same file as that when using a combination of picard reordersam + picard addorreplace, to add read groups and get correct contig order . This seems to have succeeded in terms of contig order and adding read groups, however, using GATK (DepthOfCoverage) on this 'converted' bam file I now get the error message:##### ERROR MESSAGE: Badly formed genome loc: Contig 1_gl000191_random given as location, but this contig isn't present in the Fasta sequence dictionary.

I have used the same ref fasta file in casava alignment as I have pointed gatk to (and picard when relevant), thus I don't understand why these additional/incompatible contigs are appearing. Perhaps workflow is dependant on a particualr reference file for alignment other than the one I am using (I am using human_g1k_v37.fasta reccommeded by gatk)?????

Any help would be greatly appreciated

Last edited by kingsalex; 02-14-2012 at 04:28 AM. Reason: clarity
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Old 02-14-2012, 11:47 AM   #2
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Location: USA

Join Date: Feb 2012
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Have you generated the dict file from your fasta? Make sure the fasta does not have empty lines between the chromosomes.
pzcity is offline   Reply With Quote

bam conversion, casava 1.8, gatk, picard addorreplace, picard reordersam

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