SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
BAM to VCF conversion ashwatha Bioinformatics 6 10-07-2013 07:03 AM
.bam to .wig conversion kalidaemon Bioinformatics 7 05-10-2012 02:39 PM
454 .ace to .bam conversion issue pmiguel Bioinformatics 14 06-23-2011 11:30 PM
bioscope ma to bam conversion DNAjunk Bioinformatics 1 01-14-2011 12:27 AM
Generating a BAM file from Illumina export files in CASAVa 1.7 nirav99 Bioinformatics 1 09-10-2010 01:20 AM

Reply
 
Thread Tools
Old 02-14-2012, 04:20 AM   #1
kingsalex
member
 
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
kingsalex is offline   Reply With Quote
Old 02-14-2012, 11:47 AM   #2
pzcity
Junior Member
 
Location: USA

Join Date: Feb 2012
Posts: 1
Default

Have you generated the dict file from your fasta? Make sure the fasta does not have empty lines between the chromosomes.

http://picard.sourceforge.net/comman...enceDictionary
pzcity is offline   Reply With Quote
Reply

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

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 08:15 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO