The current GATK version is 3.8-0
Examples: Monday, today, last week, Mar 26, 3/26/04

Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

Get notifications!

You can opt in to receive email notifications, for example when your questions get answered or when there are new announcements, by following the instructions given here.

Got a problem?

1. Search using the upper-right search box, e.g. using the error message.
2. Try the latest version of tools.
3. Include tool and Java versions.
4. Tell us whether you are following GATK Best Practices.
5. Include relevant details, e.g. platform, DNA- or RNA-Seq, WES (+capture kit) or WGS (PCR-free or PCR+), paired- or single-end, read length, expected average coverage, somatic data, etc.
6. For tool errors, include the error stacktrace as well as the exact command.
7. For format issues, include the result of running ValidateSamFile for BAMs or ValidateVariants for VCFs.
8. For weird results, include an illustrative example, e.g. attach IGV screenshots according to Article#5484.
9. For a seeming variant that is uncalled, include results of following Article#1235.

Did we ask for a bug report?

Then follow instructions in Article#1894.

Formatting tip!

Wrap blocks of code, error messages and BAM/VCF snippets--especially content with hashes (#)--with lines with three backticks ( ``` ) each to make a code block as demonstrated here.

Jump to another community
Download the latest Picard release at
GATK version 4.beta.3 (i.e. the third beta release) is out. See the GATK4 beta page for download and details.

Errors while running PrintReads walker of BQSR step

kssrkssr Member
edited October 2013 in Ask the GATK team

I ran BaseRecalibrator on some of my realigned bam files, there were no errors reported while running it and I was to able to generate the "recal.grp" files. However, while running the PrintReads walker to generate the recalibrated BAM files, I get the following error message for some of the BAMs.

##### ERROR MESSAGE: Exception when processing alignment for BAM index WTCHG_35305_101:4:1105:10332:129428#TGTTAACT 2/2 100b aligned read.

So, I tried to validate my realigned BAM as well as the original BAM before realignment using Picard's ValidateSAMFile and I get the following:

original BAM:
Mate unmapped flag does not match read unmapped flag of mate,
Mate alignment does not match alignment start of mate,
Mate negative strand flag does not match read negative strand flag of mate

Aditionally these errors on realigned BAMs:
Mate reference index (MRNM) does not match reference index of mate,
Mate not found for paired read

Do I need to worry about initial alignments? I read on the forums that using -rf MateSameStrand Filter should help me work around this, what does this filter exactly do? Any other approaches to solve this problem would be appreciated.

Sign In or Register to comment.