Degenerate bases in reference and variant calling with bbmap callvariants.sh
Hello, I have a reference sequence with degenerate bases (N, R etc), and would like to use callvariants to calculate all SNP frequencies in these positions. Callvariants VCF didn't show any variant calls although these SNPs are visible in IGV, and the CIGAR field shows "M" (match/mismatch) in these positions instead of "X" (using the default sam 1.4 format). Is there any way to force callvariants to recognize these calls against the unknown base as mismatches and to generate N->A,T,G,C statistics?
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