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 November 11th and 13th 2019, due to the U.S. holiday(Veteran's day) and due to a team event(Nov 13th). We will return to monitoring the GATK forum on November 12th and 14th respectively. Thank you for your patience.

Error in GATK4 MUTECT2

DioraDiora Member
edited February 2018 in Ask the GATK team

Hello
I am using RNASeq somatic mutations calls, using GATK
I got this error in somatic mutation using GATK4 Mutect::

 BAM header sample names [S1]does not contain given tumor sample name S1

This is how I assigned read groups and sample names::

 S1.dedupped.bam:  
 java -Dlog4j.configurationFile="log4j2.xml" -jar ${PICARD}/picard.jar AddOrReplaceReadGroups 
 I=${WHERE}/Aligned.out.sam O=${WHERE}/rg_added_sorted.bam \
 SO=coordinate RGID="@E00461_116_EM170602261_1" RGLB=S1_S13 RGPL=ILLUMINA 
 RGPU="@E00461_116_EM170602261_1.S1_S13" RGSM=S1

And this is the command that throw the error::

   S1.vcf.gz: S1.bam
   ${GATK4}/gatk Mutect2 \
   -R ${hg38}.fasta \
    -I S1.bam \
    -tumor S1 \
    -O S1_pon.vcf.gz

However 'S1' doesn't show in my S1.bam

Answers

  • SheilaSheila Broad InstituteMember, Broadie admin

    @Diora
    Hi,

    Can you post the BAM header that shows the @RG lines?

    Thanks,
    Sheila

  • E00461:116:GW170602261:1:2111:12713:2276 163 chr20 80381 60 151M = 80387 157 CCTTGATCCTGAATCAACAGACCACTTGCAGATATACTTCACAGCCCACGCTGACTCTGCCAAGCACAGACAACCACTGGGCCCCAGGGGAGCTGCAGGTCTCCTGGTCACCTAATCTTTTTTTTTTTTATACTTTAAGTTTTTGGGTACA @A;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;6;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;A;B;=;;;;;;=B;;;;;;;;;;;;;;;;;;;<;;;;;;;;;;=;=;BA;A=;;;;;.-B;?=A. MC:Z:151M BD:Z:OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO PG:Z:MarkDuplicates RG:Z:@E00461_116_GW170602261_1 NH:i:1 BI:Z:MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMLMMMMMMMMMMMMMLMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMLMMMMMMMMMMMMMMMMMMMMMMLMMMMMMMMMMMMM HI:i:1 nM:i:1 MQ:i:60 AS:i:298
    E00461:116:GW170602261:1:2111:12713:2276 83 chr20 80387 60 151M = 80381 -157 TCCTGAATCAACAGACCACTTGCAGATATACTTCACAGCCCACGCTGACTCTGCCAAGCACAGACAACCACTGGGCCCCAGGGGAGCTGCAGGTCTCCTGGTCACCTAATCTTTTTTTTTTTTATACTTTAAGTTTTGGGGTACATGTGCA A;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AA MC:Z:151M BD:Z:OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO PG:Z:MarkDuplicates RG:Z:@E00461_116_GW170602261_1 NH:i:1 BI:Z:MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMLMMMMMMLMMMMMMMMMMMMMMMMMMMMMM HI:i:1 nM:i:1 MQ:i:60 AS:i:298

  • SheilaSheila Broad InstituteMember, Broadie admin

    @Diora
    Hi,

    I need to see the header, not the records (so I can see what your SM tags look like). You can view the header using samtools view -H to just get the header lines.

    -Sheila

  • sorry.

    This is the @rg line in header, one sample:
    "@E00461_116_EM170602261_1" RGLB=S1_S13 RGPL=ILLUMINA
    RGPU="@E00461_116_EM170602261_1.S1_S13" RGSM=S1

  • SheilaSheila Broad InstituteMember, Broadie admin

    @Diora
    Hi,

    I am not sure whether this will help, but perhaps try removing the RGs before the LB, PL, PU and SM? Have a look at this dictionary entry for more information on setting the reads groups.

    -Sheila

Sign In or Register to comment.