I'm currently running Freebayes on tumour normal pairs to detect somatic SNPs in the tumour sample:
Raw germline calls:
freebayes -f genome.fa --pooled-discrete --genotype-qualities --read-mismatch-limit 70 \ tumour.bam normal.bam -v tn_raw.vcf
Decompose complex events into single SNPs and, tag the tumour and normal samples and quality-filter:
vcfallelicprimitives tn_raw.vcf | \ vt decompose_blocksub - | \ vt normalize -q -r genome.fa - | \ vcfsamplediff -s VT normal tumour - | \ vcffilter -f "DP > 20" \ -f "QUAL > 1 & QUAL / AO > 10" \ -f "SAF > 0 & SAR > 0" \ -f "RPR > 0 & RPL > 0" \ -f "TYPE = snp" > tn_snps_filt.vcf
Filter for somatic SNPs
vcffilter -f "VT = somatic" tn_snps_filt.vcf > tn_snps_somatic_filt.vcf
I would like to be able to include a panel of normals, and exclude any SNPs called as somatic that are present in any of the normal samples. I know that you can supply Freebayes with multiple samples, but how can I feed this information into vcfsamplediff?