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==False Negatives== * Combine output files cat fn.1Ka* > fn.1K * Compare to MAQ/SAM SNPs ../Scripts/fnCompare.pl snp.chr.txt fn.1K>fn.1Kcompare.txt * Of true SNPs (not equal to reference): {| {{table}} | Total:||10151 |- | Miss||1719 |- | Mismatch||1179 |- | Match||7253 |- | |} * Get statistics for higher coverage (8x, 20x) * Split fn file based on matching into 3 files containing only depth * To calculate # of matches with at least 8x coverage, add these two outputs: grep '^.$' fn.temp.match | grep -c '[89]' grep -c -v '^.$' fn.temp.match esult {| {{table}} | align="center" style="background:#f0f0f0;"|'''''' | align="center" style="background:#f0f0f0;"|'''Match''' | align="center" style="background:#f0f0f0;"|'''Miss''' | align="center" style="background:#f0f0f0;"|'''Mismatch''' | align="center" style="background:#f0f0f0;"|'''Total''' |- | 2x||7253||1719||1179||10151 |- | 8x||4272||179||57||4508 |- | 10x||3552||113||37||3702 |- | 20x||1580||27||3||1610 |- | |} [[Image:Fn_maqsam.jpg]] ==False Positives== * Gold standard data set: 1000 Genomes data with high coverage and quality (20 and 40) * Downloaded output of MAQ SNP filter: ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/working/20080812_ceu_trio/NA12878/ ** These should all already be different from the reference!! * From MAQ manual: "Each line consists of '''chromosome, position, reference base, consensus base, Phred-like consensus quality, read depth''', the average number of hits of reads covering this position, the highest mapping quality of the reads covering the position, the minimum consensus quality in the 3bp flanking regions at each side of the site (6bp in total), the second best call, log likelihood ratio of the second best and the third best call, and the third best call." * Parse out relevant information awk '{print $1 "\t" $2 "\t" $3 "\t" $4 "\t" $5 "\t" $6}' NA12878.snp.flt >allsnp.qd * Write Perl script to filter out coverage <20 and quality <40, convert SNPs with "oneToThree" hash ../Scripts/qrFilter.pl allsnp.qd >snp.gold ** 1,431,676 in this set * Filter by target region ../Scripts/snpInRange.pl snp.gold>snp.gold.inRange & ** Takes forever to run! ===MAQ/SAM specific=== * Filter by coverage (compare to pileup file, edit 'snpCovered.pl') ** Need to also compare to consensus: get pileup with call instead of reference awk '{print $2 "\t" $8 "\t" $4}' all.pileup>all.pileup.temp & ** Remove coverage = 1 regions grep -v ' 1 ' all.pileup.temp>pileup.noone.temp ** Convert to chromosome locations ../Scripts/convertCnsGenome.pl pileup.noone.temp>pileup.call.chr &
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