Notice:
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.
Attention:
We will be out of the office on October 14, 2019, due to the U.S. holiday. We will return to monitoring the forum on October 15.

HaplotypeCaller ERROR with ERC invalid

Hi everyone,
I'm a really novice on GATK. I want to call SNPs from 12 samples and I got some troubles.
Firstly, I combined 12 samples' bam files using the command "HaplotypeCaller". Each bam file stands for one sample and is generated by two PE sequencing files (R1 & R2). However, I got the ERROR:

A USER ERROR has occurred: Argument --emitRefConfidence has a bad value: Can only be used in single sample mode currently. Use the sample_name argument to run on a single sample out of a multi-sample BAM file.

Refer to the problem before,it seems that the BAM file has multiple lanes message. I checked the SAM file's head lines and tail lines. The head lines are as following:
HWI-7001446:625:C9078ANXX:6:1101:1209:2074 ……
HWI-7001446:625:C9078ANXX:6:1101:1209:2074 ……
HWI-7001446:625:C9078ANXX:6:1101:1232:2088 ……
HWI-7001446:625:C9078ANXX:6:1101:1232:2088 ……
And the tail lines are as following:
ST-E00159:217:HYL2KCCXX:6:2224:23979:72667 ……
ST-E00159:217:HYL2KCCXX:6:2224:23979:72667 ……
ST-E00159:217:HYL2KCCXX:6:2224:24000:72667 ……
ST-E00159:217:HYL2KCCXX:6:2224:24000:72667 ……

Next, I format the BAM file by the command "AddOrReplaceReadGroups". Then I run the HaplotypeCaller command on the formated BAM file. The .g.vcf file has been generated and I got another ERROR:

A USER ERROR has occurred: Traversal by intervals was requested but some input files are not indexed.
Please index all input files:
samtools index xxx.group.bam

Is the generated .g.vcf file valid? Why did I get the two ERROR messages?

Thank u very much.

Best wishes,

Tony

Tagged:

Best Answer

  • Accepted Answer

    Besides, the formated BAM file is similar to the initial BAM file. I have checked the formated BAM file's SAM file. In fact, it seems that it has been added several lines:
    The 1st line: @HD VN:1.5 SO:unsorted
    The last line before "alignment section": @RG ID:4 LB:lib1 PL:illumina SM:20 PU:unit1
    And other lines look the same……
    The head lines and tail lines are still different as he initial SAM file.

Answers

  • Tony_LeeTony_Lee Member
    Accepted Answer

    Besides, the formated BAM file is similar to the initial BAM file. I have checked the formated BAM file's SAM file. In fact, it seems that it has been added several lines:
    The 1st line: @HD VN:1.5 SO:unsorted
    The last line before "alignment section": @RG ID:4 LB:lib1 PL:illumina SM:20 PU:unit1
    And other lines look the same……
    The head lines and tail lines are still different as he initial SAM file.

  • SheilaSheila admin Broad InstituteMember, Broadie, Moderator admin

    @Tony_Lee
    Hi Tony,

    The error message suggests your BAM files are not indexed. You need to use samtools index to index them.

    -Sheila

Sign In or Register to comment.