How to build/get populationAlleleFrequencies.vcf for ContEst ?
and what is the necessary field of VCF file? AF field? MAF field?
I found no guide for this. and I tried 1000G vcf file, but it failed with the following error.
java -jar /usr/hpc-bio/gatk/GATK.jar -T ContEst -l WARN -R /usr/bio-ref/GRCh38.83/GRCh38.dna.fa -pf /usr/bio-ref/GRCh38.83/1000G.vcf -isr INTERSECTION -I:eval /biowrk/bam.bqsr.pair/Project_14686/Sample_100T/bqsr.tumor.bam -I:genotype /biowrk/bam.bqsr.pair/Project_14686/Sample_100T/bqsr.normal.bam -L /usr/bio-ref/GRCh38.83/S04380110_Covered.intervals -o output.txt
ERROR ------------------------------------------------------------------------------------------
ERROR stack trace
java.lang.NullPointerException
at org.broadinstitute.gatk.tools.walkers.cancer.contamination.ContEst.calcStats(ContEst.java:625)
at org.broadinstitute.gatk.tools.walkers.cancer.contamination.ContEst.map(ContEst.java:400)
at org.broadinstitute.gatk.tools.walkers.cancer.contamination.ContEst.map(ContEst.java:127)