LUMPY(1)

💅 LUMPY — ok bestie, let's find some structural variants

Heyyy so you're reading the manual page for lumpy, aka LUMPY, living in the User Commands section of the manual. Automated breakpoint detection for standard analyses — that's the whole vibe. Let's get into it. 🦋

✨ NAME ✨

lumpy — Automated breakpoint detection for standard analyses

🌸 SYNOPSIS 🌸

lumpy [OPTIONS]

That's it. That's the whole synopsis. She's a simple girl with a lot of flags. 💅

🧚 DESCRIPTION 🧚

So LUMPY is a novel SV discovery framework (structural variants, bestie, not student version 💀) and the way it works is that it naturally integrates multiple SV signals jointly across multiple samples. That's the whole main character move.

And the payoff? LUMPY yields improved sensitivity 🔥 — especially when the SV signal is reduced, which happens either because you've got low coverage data or because your intra-sample variant allele frequency is low. Basically when the signal is giving nothing, LUMPY still shows up and eats. 👑

✨ OPTIONS ✨

Every single one, no skips, no shortcuts. Let's go. 🌈

• -g — Genome file (this is what defines chromosome order, so be nice to it)
• -e — Show evidence for each call. Receipts! 🧾
• -w — File read windows size (default 1000000)
• -mw — minimum weight for a call
• -msw — minimum per-sample weight for a call
• -tt — trim threshold
• -x — exclude file bed file
• -t — temp file prefix, must be to a writeable directory ⚠️ (yes, it has to actually be writeable, do not play with her)
• -P — output probability curve for each variant 📈
• -b — output BEDPE instead of VCF
• -sr — split read settings, and she takes a whole little list of them:

bam_file:<file name>,
id:<sample name>,
back_distance:<distance>,
min_mapping_threshold:<mapping quality>,
weight:<sample weight>,
min_clip:<minimum clip length>,
read_group:<string>

• -pe — paired end settings, and she takes an even longer list:

bam_file:<file name>,
id:<sample name>,
histo_file:<file name>,
mean:<value>,
stdev:<value>,
read_length:<length>,
min_non_overlap:<length>,
discordant_z:<z value>,
back_distance:<distance>,
min_mapping_threshold:<mapping quality>,
weight:<sample weight>,
read_group:<string>

• -bedpe — bedpe input, and here's her list:

bedpe_file:<bedpe file>,
id:<sample name>, weight:<sample weight>

💖 AUTHOR 💖

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. Giving credit where credit is due, periodt. 🫶

ok that's the whole page, you're fully certified now 💜 go call some variants

Signing off for real: this is lumpy 0.3.0, dated June 2020, and that's the LUMPY(1) energy. bye bestie, slay your breakpoints 🌟