We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Picard ReorderSam Error: Read CIGAR M operator maps off end of reference
Origin of the problem:
GATK detected different order of the bam file and the reference file as follows:
ERROR MESSAGE: Input files reads and reference have incompatible contigs: The contig order in reads and referenceis not the same; to fix this please see: (https://www.broadinstitute.org/gatk/guide/article?id=1328), which describes reordering contigs in BAM and VCF files..
ERROR reads contigs = [1, 2, 3, 4, 5, 6, 7, 8, 9, X, Y, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, MT, NT_113887, ...]
ERROR reference contigs = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, X, Y, MT, NT_113887, ...]
Then I referred to the link, https://www.broadinstitute.org/gatk/guide/article?id=1328
And decided to use Picard ReorderSam tool, which led me to the issue reported here,
The Problem: Picard ReorderSam terminates with error.
java -Xmx110g -Djava.io.tmpdir=$workDir/merged-bams/tmp -jar ./picard/1.115/ReorderSam.jar ALLOW_INCOMPLETE_DICT_CONCORDANCE=true
INFO 2015-12-09 12:24:39 ReorderSam Writing reads...
INFO 2015-12-09 12:24:39 ReorderSam Processing All reads
[Wed Dec 09 13:20:08 CST 2015] picard.sam.ReorderSam done. Elapsed time: 55.49 minutes.
To get help, see http://picard.sourceforge.net/index.shtml#GettingHelp
Exception in thread "main" htsjdk.samtools.SAMFormatException: SAM validation error: ERROR: Read name HWUSI-EAS1612_61FV6:6:91:1510:1207#0, Read CIGAR M operator maps off end of reference
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[bam_index_core] Invalid BAM header.[bam_index_build2] fail to index the BAM file.
Attempts to fix:
1. I performed Picard CleanSam to solve this error:
java -Xmx56g -jar ./picard/1.115/CleanSam.jar I=$workDir/merged-bams/$sample.sorted.bam O=$workDir/merged-bams/$sample.sorted.cleaned.bam
And the output is attached.
2. Then reordering this cleaned sam also throws the same error as mentioned above.
3. Next I performed Picard ValidateSamfile and the log contains the readnames with error"Read CIGAR M operator maps off end of reference"
Can you please help me get around this issue? All I really want is proceed with GATK having same order of bam and reference contigs.
I have been referring vigorously to several GATK discussions, but none addresses this issues directly or has helped find a solution.