Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
samtools picard SamFormatConverter Bio.X2Y Bioinformatics 3 07-08-2013 08:46 AM
Picard and GATK poisson200 Bioinformatics 6 08-15-2012 08:04 AM
ReorderSam.jar in picard and GATK wisekh Bioinformatics 0 12-12-2011 08:27 AM
Errors from Picard and GATK on a BWA paired-end BAM oiiio Bioinformatics 2 12-07-2011 08:50 PM
samtools vs picard index pallo Bioinformatics 1 04-11-2011 04:59 PM

Thread Tools
Old 07-11-2012, 09:25 AM   #1
Location: USA

Join Date: Nov 2010
Posts: 56
Default Who is the culprit? Picard, Samtools or GATK?


I am using RNA-Seq data and my work flow is below..and am having trouble with BAM file

Single end fastq->Shrimp alignment->sam file->changed to BAM using Samtools->added read groups using Picard->index and Now fed this into GATK-> works fine.

In best practice of GATK v3, they ask you to combine all your BAM files. So i took the bam files after read group were added using Picard -> Picard Mark duplicates->Mergesamfiles(BAM can be input too)->index the file and the Validate BAM file-> result (No errors found). I did not get any error in all these steps.

Now the combined BAM files fail to be recognized by GATK throwing an error "ERROR MESSAGE: Bad input: Could not find any usable data in the input BAM file(s)."

I looked at the BAM files using IGV viewer and it looks fine and all the read have read groups and quality of 255.

1) so why is GATK doing it? Is there a problem with my BAM? Any ideas?

I was reading in GATK forum and found an explaination as to why it happens by a user " In my experience, some mapping program do not calculate map Quality score correctly, it will output 255 as mapping score, but 255 actually in GATK's CountCovariatesWalker is filtered out by MappingQualityUnavailableFilter in the top of walker:
@ReadFilters({MappingQualityZeroFilter.class, MappingQualityUnavailableFilter.class})
just get rid of MappingQualityUnavailableFilter.class in this line, then it will works...(this works for my case..)"

2) HAs anybody noticed it?

newbietonextgen is offline   Reply With Quote
Old 07-16-2012, 01:39 PM   #2
Junior Member
Location: Toronto

Join Date: Oct 2011
Posts: 3

Did SHRiMP compute mapping qualities? Look in an output file, if you see any MQV of 255, then the answer is NO.

If the answer is YES, some program down the line must have lost them somehow.

If the answer is NO, you have to rerun the mappings. Find out which option disabled MQVs in SHRiMP, and disable it or work around it.
-- Matei David
mateidavid is offline   Reply With Quote
Old 07-16-2012, 06:47 PM   #3
Location: USA

Join Date: Nov 2010
Posts: 56

Shrimp worked well. I thinks its some program down the line that goofed the results. For now i just am using a different approach (Freebayes) and no problems yet..
newbietonextgen is offline   Reply With Quote

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 08:12 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO