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Interpret MuTect result

y.songy.song Seoul, KoreaMember

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 :)

Caroline Song.


Best Answers


  • y.songy.song Seoul, KoreaMember

    Dear @shlee

    Thanks for your help. It was helpful for me to understand what is the meaning of each columns. However, the definition of context is not mentioned on the webpage which you've posted. I tried to find it out on the google, but it did not work that well. Could you explain to me about that column if it is okay? Thanks in advance for your help :)

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