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===Plan outline=== *Going to use combination of CIGAR string, baseQuality, and readBases with matching bases replaced with '=' (using samtools calmd -e) because easier to parse **Could parse MD tag in sam file to count ins/del/subs of each mapped read **Could use NM (edit distance to the reference) to see how many changes necessary to make read equal to reference **Could also use mpileup *Going to convert CIGAR string into a string with length equal to readBases (example: 5M1I6M -> MMMMMIMMMMMM) to determine if readBases letter is a insertion or substitution **Any base index of a read with substitution error can be checked with the base quality scores to see if quality score is >= 20 (Phred33 scale) #Turn sam -> bam #Sort bam file #Index sorted bam file #Filter out unmapped reads and mapped reads with MAPQ < 8 (16% alignment is wrong - [http://maq.sourceforge.net/qual.shtml Understanding Mapping Quality]) #Remove ':' from probe names in sam file and reference fasta file (Because ':' is used by samtools to signify end of contig name) #Replace any matched bases in readBases line to '=' #Count ins/del/subs with Count_mismatches_from_SAMwEquals_quantifyOligov2.pl into 7 categories: perfect match | 1 ins/del | 1 sub | 2 ins/del | 2 sub | 1 ins/del & 1 sub | 3+ mismatches #Count up every error and divide by total number of bases: Error rate is output to command line
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