I used the command you suggested above to call somatic variants in tumor-normal pairs, and the resulting VCF file named, 'freebayes_pooled-discrete.vcf' had
##INFO=<ID=SSC,Number=1,Type=Float,Description="Somatic variant score (phred-scaled probability that the somatic variant call is correct).">
However, looking at some of the data lines and using 'grep SSC
freebayes_pooled-discrete.vcf', none of the called variants had the
Somatic variant score (SSC). Could you be knowing why this is so? The exact command line I used was:
freebayes --no-indels --no-mnps --no-complex -f hg19.fa --pooled-discrete --genotype-qualities normal.bam tumor.bam | ./vcfsamplediff -s VT normal.bam tumor.bam - | ./vcffilter -f "QUAL > 20" > freebayes_pooled-discrete.vcf
Also, I am using muTect and it has PASS and SOMATIC defined as:
##FILTER=<ID=PASS,Description="Accept as a confident somatic mutation">
How do these compare with freebayes as I used it? I am trying to
determine which parameters will best make freebayes and muTect
comparable when it comes to calling somatic point mutations.
The muTect command I used is:
java -Xmx2g -jar muTect-1.1.4.jar --analysis_type MuTect --reference_sequence hg19.fa --dbsnp dbsnp_137.hg19.vcf --input_file:normal normal.bam --input_file:tumor tumor.bam --out mutect_results.txt --coverage_file mutect_coverage.wig --enable_extended_output --vcf mutect_results_extended.vcf
Would really appreciate your advice!