One normal sample. Do I create a panel of normals? I want to run tumor-only mode, in mouse samples
REQUIRED for all errors and issues:
a) GATK version used: v4.4.0.0
b) Exact command used:
gatk Mutect2 -R reference.fasta -I normal1.bam -max-mnp-distance 0 -O normal1.vcf.gz
This comand worked perfectly
gatk GenomicsDBImport -R reference.fasta -L intervals.interval_list \
--genomicsdb-workspace-path pon_db \
-V normal1.vcf.gz \
-V normal2.vcf.gz \
-V normal3.vcf.gz
then tried this with one sample only, but an error occur mentioning that the genome loc coordinates exceeded the contig size, the -R parameter was the same in both comands, and the -L I provided the covered.bed by the manufacturer. However, is there a problem if the -R is a reference updated and the bed file is not.
My question is if I need to creat a panel of normals if i only have one sample.
-
For inbred species such as mice you can use a single normal sample as a matched normal for your tumor cases therefore you don't have to deal with a PoN.
Regards.
-
Even if the tumor samples, are from diferent mice? I have 8 tumor samples, from 8 different mice. Is it correct to match all to the same normal sample?
-
If all mice are of the same species including the induced tumors then it should be fine since those mice are inbred and their variance will be quite limited in germline.
-
Thank you very much for the answer.
Paulo
Please sign in to leave a comment.
4 comments