Hi,
I am using VariantsToTable to populate the vcf to a table.
the vcf file was generated by:
samtools mpileup -Q 20 -q 10 --skip-indels -f Homo_sapiens_assembly19.fasta -l ${merged_mutations} -v -t DP,AD,ADF,ADR,SP -o "${oprefix}".vcf.gz ${Normal_bam} ${Tumor_bam}
I feed normal_bam then tumor_bam.
java -jar /scratch/genomic_med/apps/gatk/default/GenomeAnalysisTK.jar \
-R /scratch/rists/hpcapps/reference/human/broad_hg19/fastas/Homo_sapiens_assembly19.fasta \
-T VariantsToTable \
-V "${oprefix}".vcf.gz \
--allowMissingData \
--showFiltered \
-F CHROM -F POS -F REF -F ALT -F QUAL -F DP -GF PL -GF DP -GF SP -GF AD -GF ADF -GF ADR \
-o "${oprefix}".table
What I found strange is that, sometimes, the output table put tumor_bam associated values before the normal_bam associated values, and sometimes put them after the normal_bam. How does VariantsToTable determine the ordering?
Thanks!
Ming