Wondering if anyone has run into a similar issue. I tried running lofreq with the call option:
lofreq call -s -S /path/to/dbsnp_147_b37_common_all_20160601.vcf -f \ /path/to/Homo_sapiens_assembly19.fasta -o /path/to/output.vcf /path/to/tumor_bam.bam
However, I do not see any calls, and I only see a VCF header in output.vcf. All that is in the log is:
Number of substitution tests performed: 0 Number of indel tests performed: 0
Is there a reason why this might be?