Entering edit mode
6.8 years ago
Tania
▴
180
Hi Everyone
If we don't have normal-tumor matched sample.
Is it reasonable to run tumor against PON with no nomral input. Like I want to compare the Tumor to the PON not to specific normal sample.
Like this, with no normal input (-I:normal
) just the tumor sample and the PON
java -jar ${GATK}/GenomeAnalysisTK.jar -T MuTect2 \
-I:tumor tumor1.bam \
--dbsnp ${DBSNP} \
--cosmic ${COSMIC} \
--normal_panel pon_siteonly.vcf.gz \
--output_mode EMIT_VARIANTS_ONLY \
-o tumor1.vcf.gz \
-R ${hg38}.fasta
Thanks