**0**wrote:

Dear Users,

I tried to detect SNV and indel using Mutect2, as below;

```
java -Xmx4g -jar /path/to/gatk-4.0.0.0/gatk-package-4.0.0.0-local.jar Mutect2
--input normal_rmdup-realgin.bam tumor_rmdup-realign.bam --output mutect.vcf
--tumor-sample tumor_rmdup-realign.bam -R ~/home/path/to/hg19genome.fa
```

then, the error has occured "A USER ERROR has occurred: Bad input: BAM header sample names [whatever]does not contain given tumor sample name tumor_rmdup-realign.bam" (Note:'normal' and 'tumor' are other names, and directory name is changed, practically.)

I'd like to know the reason of this error, the header of BAM is invalid?

the header of BAM shows below

```
@HD VN:1.4 GO:none SO:coordinate
@SQ SN:chrM LN:16571
@SQ SN:chr1 LN:249250621
@SQ SN:chr2 LN:243199373
@SQ SN:chr3 LN:198022430
@SQ SN:chr4 LN:191154276
@SQ SN:chr5 LN:180915260
@SQ SN:chr6 LN:171115067
@SQ SN:chr7 LN:159138663
@SQ SN:chr8 LN:146364022
@SQ SN:chr9 LN:141213431
@SQ SN:chr10 LN:135534747
@SQ SN:chr11 LN:135006516
@SQ SN:chr12 LN:133851895
@SQ SN:chr13 LN:115169878
@SQ SN:chr14 LN:107349540
@SQ SN:chr15 LN:102531392
@SQ SN:chr16 LN:90354753
@SQ SN:chr17 LN:81195210
@SQ SN:chr18 LN:78077248
@SQ SN:chr19 LN:59128983
@SQ SN:chr20 LN:63025520
@SQ SN:chr21 LN:48129895
@SQ SN:chr22 LN:51304566
@SQ SN:chrX LN:155270560
@SQ SN:chrY LN:59373566
@RG ID:1 PU:whatever LB:whatever SM:whatever PL:illumina
@PG ID:bwa VN:0.7.12-r1039 CL:/bin/bwa mem /path/to/hg19genome.fa /home/path/to/tumor_R1.fastq.gz /home/path/to/tumor_R2.fastq.gz PN:bwa
@PG ID:GATK IndelRealigner CL:knownAlleles=[] targetIntervals=tumor_rmdup.intervals LODThresholdForCleaning=5.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=150000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=20000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null
```

I'd appreciate giving kindness, thanks.

Sincerely.

**120**• written 19 months ago by m-hayashi •

**0**

Have you tried the GATK forum ?

820Thank you for reply, but not yet.

0