VARCALL(1)

👑 NAME

varcall — ea-utils: output summry stats or perform variant calling 💅

(not a typo of mine, bestie, that's literally how the original spells "summry" and I am not the one who's gonna touch it)

✨ SYNOPSIS ✨

varcall <-s|-v> <-f REF> [options] bam1 [bam2...]

🦋 DESCRIPTION

Version: 0.9.632 (BETA)

Okay so here's the vibe: this thing either outputs summry stats for the list of files, or it performs variant calling. Pick your fighter. 🎀

Options (later options override earlier) — yes, so if you say the same thing twice, the last one wins, main character energy, periodt:

• -s — Calculate statistics 📊
• -v — Calculate variants bases on supplied parameters (peep -S)
• -f — Reference fasta (required if using bams, ignored otherwise)
• -m — Min locii depth (default 0)
• -a — Min allele depth (default 0)
• -p — Min allele pct by quality (default 0)
• -q — Min qual (default 3)
• -Q — Min mapping quality (default 0)
• -b — Min pct balance (strand/total) (default 0)
• -D FLOAT — Max duplicate read fraction (depth/length per position) (default 1)
• -B — Turn off BAQ correction (default false)
• -R — Homopolymer repeat indel filtering (default 8)
• -e FLOAT — Alpha filter to use, requires -l or -S (default .05)
• -g FLOAT — Global minimum error rate (default: assume phred is ok) 🙈
• -l INT — Number of locii in total pileup used for bonferroni (default 1 mil)
• -x CHR:POS — Output this pos only, then quit ✌️
• -N FIL — Output noise stats to FIL
• -S FIL — Read in statistics and params from a previous run with -s (do this!) 🔥
• -A ANNOT — Calculate in-target stats using the annotation file (requires -o)
• -o PREFIX — Output prefix (note: overlaps with -N)

🌸 Input files

Files must be sorted bam files with bai index files available. Alternatively, a single pileup file can be supplied. That's the whole menu, no substitutions. 🍓

💖 Output files

Varcalls go to stdout. Stats go to stdout, or stderr if varcalling too. Yes bestie, they share a stream, keep up. 👑

🧚 If an output prefix is used, files are created as follows:

• PREFIX.var — Variant calls in tab delimited 'varcall' format
• PREFIX.eav — Variant calls in tab delimited 'ea-var' format
• PREFIX.vcf — Variant calls, in vcf format
• PREFIX.varsum — Summary of variant calls
• PREFIX.tgt — On-target stats detail
• PREFIX.tgtsum — Summary of on-target stats
• PREFIX.noise — Noise stats detail

🌈 Stats Output:

Contains mean, median, quartile information for depth, base quality, read len, mapping quality, indel levels. Also estimates parameters suitable for variant calls, and can be passed directly to this program for variant calls. So you run it once, it does its little statistical dance, and then it feeds itself. Self-care, honestly. ✨

💀 Filtering Details:

Nothing. Empty. A heading with no content. It's giving mystery, it's giving the void. Not me adding anything to it either, because I refuse to make stuff up about filters that the page never describes. 🫶

Okay that's the whole page, bestie — every flag, every default, every file, nothing skipped, no cap. This was varcall 1.1.2, from July 2015, living its User Commands life. Go call some variants. Slay. 💜