|
|
|
|
|||||||
Similar Threads
|
||||
| Thread | Thread Starter | Forum | Replies | Last Post |
| Convert merged BAM back to per lane BAM or FASTQ file | danielsbrewer | Bioinformatics | 6 | 10-03-2013 08:29 AM |
| Where can I get GM19240 HapMap cell line variant calls as VCF or a BED file | adrian | Bioinformatics | 2 | 09-13-2012 02:27 AM |
| Obtaining strand calls from BAM/SAM | Protaeus | Bioinformatics | 1 | 06-06-2011 05:07 PM |
| maq 2nd and 3rd likely SNP Calls | AnamikaDarwin | Bioinformatics | 0 | 07-24-2009 09:00 AM |
| Maq SNP calls from a large pool | mimi_lupton | Bioinformatics | 0 | 10-31-2008 09:48 AM |
 |
|
|
Thread Tools |
02-08-2012, 08:02 AM
|
#1 |
|
Member
Location: UK Join Date: Nov 2010
Posts: 49
|
How to quickly rewrite MAQ calls in bam file
I was wondering if there is any swift solution to this problem. I am using bowtie to align my reads and it turns that all MAQ=255. This in turn causes GATK to drop all my calls.
GATK suggested to rewrite bam file with new MAQ scores (lets say 60). -rf ReassignMappingQuality -DCQ 60 is discontinued for GATK1.4 and older versions (<1.4) return "exception faults". Any ideas ? |
|
|
|
02-08-2012, 09:19 AM
|
#2 |
|
Member
Location: UK Join Date: Nov 2010
Posts: 49
|
if anyone would be interested here is solution (at least it worked for me):
java -jar GenomeAnalysisTK.jar -T PrintReads -rf ReassignMappingQuality -DMQ 60 -R reference.fasta -I input.bam -o output.bam |
|
|
|
|
| Thread Tools | |
|
|
