Can we omit the normal input and compare tumor to pon only in MuTect2?
0
0
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

Tumor RNA-Seq mutect • 1.8k views
ADD COMMENT

Login before adding your answer.

Traffic: 1020 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6