Can I specify the name of the sample in the header of the VCF created with Pisces

[Manuel-DominguezCBG]

I was wondering if something like this is possible

apptainer exec --bind /mnt:/mnt docker://trinhanne/pisces:5.2.10 dotnet /app/Pisces_5.2.10.49/Pisces.dll \
               -bam "$RunID"_"$Sample_Name".bam  \
               -g  "$genomedirectory" \
               -o ./ \
               -i "$ampliconscoordenatesbed"  \
               --gvcf false \
               --minvq 20 \
               --maxvq 100 \
               --minbq 20 \
               --mindpfilter 500 \
               --ssfilter False \
               --minmq 20 \
               --mindp 10 \
               --sample "$Sample_Name"

This command works apart from the --sample with return

Unsupported options:
   --sample

The reason I am doing this is because after running Pisces, I use this

apptainer exec --bind /mnt:/mnt docker://mgibio/bcftools-cwl:1.12 bcftools annotate \ -a "$ampliconscoordenatesbed" \ -c CHROM,FROM,TO,4 \ -h "$RunID"_"$SampleName".vcf \ -x FORMAT/SB "$RunID""$SampleName".vcf > "$RunID""$Sample_Name"_FINAL.vcf

to remove the SB flag and to add the amplicon name (from the bed file) in the VCF file. However, I get this error

Could not parse 240430_M01875_1088_000000000-LH8PT_W2407562-002.vcf: #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 240430_M01875_1088_000000000-LH8PT_W2407562-002.bam

I think this is due to the ".bam" I want to remove from the header. How can I do this.

[Manuel-DominguezCBG]

I have closed this issue at the moment. I will open this is I cannot find the solution.