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