Can we omit the normal input and compare tumor to pon only in MuTect2?
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6.3 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

Tumor RNA-Seq mutect • 1.8k views
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