Interpret MuTect result
After running MuTect, to extract the SNP data, I used these set of commands.
/usr/lib/jvm/java-8-openjdk-amd64/bin/java -Xmx4g -jar /share/tools/muTect/mutect-1.1.7.jar --analysis_type MuTect --reference_sequence /share/projects/NCC_WGS/reference/ucsc.hg19.fasta --cosmic /share/projects/NCC_WGS/1000G/b37_cosmic_v54_convert_ucsc_hg19.vcf --dbsnp dbsnp_132_b37.leftAligned_convert_ucsc_hg19.vcf --input_file:normal N7_dupRemoved_realigned_fixed_recalib.bam --input_file:tumor C7_dupRemoved_realigned_fixed_recalib.bam --out call_stats_GC7.out --coverage_file coverage_sample.wig.txt --vcf GC7_out.vcf
grep -v 'REJECT' call_stats_GC7.out > GC7_SNP.txt
On the data, I have some problems to understand some columns. The data started like as below.
Contig Position Context Ref_allele alt_allele .... score dbsnp_covered power tumor_power normal_power
On these columns, although I searched on the forum, these are still difficult to understand: context, score, dbsnp_sote, covered, tumor_power and normal_power.
Could you explain to me in easier way? Thanks in advance