EXACTSNP(1)

✨ NAME ✨

bestie, you're reading the EXACTSNP(1) manual, and the star of the show is exactSNP — a toolkit for processing next-gen sequencing data. that's the whole vibe. 🧬💖

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🌸 DESCRIPTION 🌸

Version 2.0.4

okay so the usage is literally:

./exactSNP [options] -i input -g reference_genome -o output

💖 Required arguments

• -i <file> — bestie, this is where you drop the name of your input file that has the read mapping results. the format can be SAM or BAM. and if it's BAM, you have to pass -b too. (the original says: The [-b if BAM] format of input file can be SAM or BAM (-b needs to be specified if a BAM file is provided).) 🫶
• -g <file> — specify the name of the file that includes all reference sequences. only one single FASTA format file should be provided. no more, no less. ✨
• -o <file> — specify the name of the output file. this program outputs a VCF format file that includes discovered SNPs. so slay. 💅

🎀 Optional arguments

• -a <file> — provide a set of annotated SNPs (like the ones in the dbSNP database). the supplied file should be in VCF format (gzipped file is accepted, love that). providing known SNPs to the program should improve its SNP calling performance. note that the provided SNPs may or may not be called. 🤷‍♀️
• -b — indicate the input file provided via -i is in BAM format. that's it, that's the flag. 🌈
• -Q <int> — specify the q-value cutoff for SNP calling at sequencing depth of 50X. 12 by default. the corresponding p-value cutoff is 10^(-1*Q). note that this program automatically adjusts the q-value cutoff according to the sequencing depth at each chromosomal location. so it's lowkey smart. 🔥
• -f <float> — specify the minimum fraction of mis-matched bases a SNP-containing location must have. its value must be between 0 and 1. 0 by default. 🍓
• -n <int> — specify the minimum number of mis-matched bases a SNP-containing location must have. 1 by default. 💜
• -r <int> — specify the minimum number of mapped reads a SNP-containing location must have (ie. the minimum coverage). 1 by default. 👑
• -x <int> — specify the maximum depth a SNP location is allowed to have. 1,000,000 reads by default. this option is useful for removing PCR artefacts. so if your data is extra, this is your bestie. 😭
• -s <int> — specify the minimum base quality scores (Phred scores) read bases must satisfy to be used for SNP calling. 13 by default. read bases with quality scores less than 13 will be excluded from the analysis. periodt. 💀
• -t <int> — specify the number of bases trimmed off from each end of the read. 3 by default. ✂️
• -T <int> — specify the number of threads. 1 by default. multitasking queen. 🧵
• -v — output version of the program. short and sweet. 🌟
• -C <path> — specify the path to save the temporary files. keep your temp files cute and organized. 🎀

🌈 Example

./exactSNP -i my-alignment.sam -g mm10.fa -o my-SNPs.txt

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👑 AUTHOR 👑

this manpage was written by Alexandre Mestiashvili for the Debian distribution and can be used for any other usage of the program. iconic. 💖

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and that's the whole page, bestie! this was exactSNP 2.0.3, from March 2023, and it's the EXACTSNP(1) manual. byeeee ✨🦋💅