Dear Sheila, and Geraldine,
would appreciate your input about understanding please the output from contEST that i run on normal-tumor pair :
the results look in the following way (below) and the question is : the 4% contamination represents the cross-patient contamination, OR the actual % of normal cells in the tumor sample ? many thanks !
name population population_fit contamination confidence_interval_95_width confidence_interval_95_low confidence_interval_95_high sites
META CEU n/a 4.0 1.5 3.3 4.8 22
the command is :
$GATK \
-T ContEst \
-R $REFERENCE \
-I:eval $TUMOR_MD \
-I:genotype $NORMAL_MD \
-L $CHR \
--popfile $POPFILE \
-isr INTERSECTION \
-o "vcf.check-CONTAMINATION.${TUMOR_MD%.bam}vs${NORMAL_MD%.bam}on${CHR}.analysis-ContEST.txt" \
--disable_auto_index_creation_and_locking_when_reading_rods
where the POPFILE is "hg19_population_stratified_af_hapmap_3.3.vcf.with-chr.converted-to-hg38".