JGI_SUMMARIZ...CONTIG_DEPTHS(1)

✨ JGI_SUMMARIZE_BAM_CONTIG_DEPTHS ✨

okay bestie, welcome to the User Commands section of the manual, where we talk about jgi_summarize_bam_contig_depths 💅 this is the whole vibe, no cap.

🌸 NAME 🌸

jgi_summarize_bam_contig_depths — jgi_summarize_bam_contig_depths nosha

like... that's the name, that's the whole thing, periodt.

🦋 SYNOPSIS 🦋

jgi_summarize_bam_contig_depths <options> sortedBam1 [ sortedBam2 ...]

so you're handing it <options> and then one or more sorted bams — sortedBam1, and if you're feeling extra, sortedBam2 ... and beyond 🫶

💖 OPTIONS 💖

• --outputDepth arg — this is where the contig-by-bam depth matrix goes. the default is STDOUT, so if you don't say anything it just yells the matrix right at your terminal, iconic behavior honestly.
• --percentIdentity arg — the minimum end-to-end % identity a read needs to qualify (default: 97). mid reads need not apply 🙈
• --pairedContigs arg — the file where the sparse matrix of contigs that paired reads span gets written (default: none).
• --unmappedFastq arg — the prefix for dumping unmapped reads out of every bam file. it gets suffixed by bamfile.bam.fastq.gz, so don't @ me about the naming.
• --noIntraDepthVariance — do not include variance from mean depth along the contig. just... no variance. none. we're keeping it simple.
• --showDepth — outputs a .depth file per bam, for each contig base. every single base. she's thorough like that 💅
• --minMapQual arg — the minimum mapping quality needed for a read to count as mapped (default: 0).
• --weightMapQual arg — weights the per-base depth based on the MQ of the read (i.e. its uniqueness). default: 0.0 which means disabled (default: 0.0 (disabled)).
• --includeEdgeBases — when calculating depth & variance, include the 1-readlength edges. it's off by default, so you gotta opt in bestie.
• --maxEdgeBases — when calculating depth & variance and you did not pass --includeEdgeBases, this is the maximum length (default: 75).
• --referenceFasta arg — the reference file. ⚠️ it must be the same fasta that the bams used, no substitutions, no swaps, fr fr.

🌈 Options that require a --referenceFasta 🌈

like the heading says, these ones need a --referenceFasta to even function, so bring your fasta or go home 🎀

• --outputGC arg — the file to print the gc coverage histogram to.
• --gcWindow arg — the sliding window size used for GC calculations.
• --outputReadStats arg — the file to print the per-read statistics to.
• --outputKmers arg — the file to print the perfect kmer counts to.

💜 Options to control shredding contigs that are under represented by the reads 💜

shredding era 😭 these ones decide how contigs that the reads are lowkey ignoring get chopped up.

• --shredLength arg — the maximum length of the shreds.
• --shredDepth arg — the depth at which to generate overlapping shreds.
• --minContigLength arg — the mimimum length of contig to include for mapping and shredding. (yes, that's spelled mimimum in the original and I am simply not going to pretend otherwise 🙈)
• --minContigDepth arg — the minimum depth along the contig at which to break the contig.

👑 AUTHOR 👑

this manpage was written by Andreas Tille for the Debian distribution, and it can be used for any other usage of the program 🫶 slay.

and that's the whole page, bestie ✨ this was jgi_summarize_bam_contig_depths from May 2020, filed under JGI_SUMMARIZ...CONTIG_DEPTHS(1) — go forth and summarize those depths, you absolute main character 🦋💖