Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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