SAMBLASTER:(1)

💖 SAMBLASTER:(1) 💖

okay bestie, welcome to the User Commands section of the manual, and this one? this one is samblaster: — the post-processing queen for your aligner output (bwa mem girlies, this is for you) 💅

✨ NAME ✨

samblaster: — post processing on an aligner (eg. bwa mem):

🌸 SYNOPSIS 🌸

bwa mem <idxbase> samp.r1.fq samp.r2.fq | samblaster [-e] [-d
samp.disc.sam] [-s samp.split.sam] | samtools view -Sb - > samp.out.bam
bwa mem -M <idxbase> samp.r1.fq samp.r2.fq | samblaster -M [-e] [-d
samp.disc.sam] [-s samp.split.sam] | samtools view -Sb - > samp.out.bam

🦋 DESCRIPTION 🦋

so basically, this tool marks duplicates for you, and if you want, it can also spit out split reads and/or discordant pairs. the way that it just handles all of that?? iconic. ✨

⚠️ your input sam file must contain paired end data, must contain a sequence header, and must be sorted by read ids. no cap, it will not play with you otherwise.

the output is literally every alignment in the exact same order as the input, with duplicates marked with FLAG 0x400. periodt. 💜

🎀 For use with a pre-existing bam file to pull split, discordant and/or unmapped reads:

samtools view -h samp.bam | samblaster [-a] [-e] [-d
samp.disc.sam] [-s samp.split.sam] [-u samp.umc.fasta] -o
/dev/null

💅 OPTIONS 💅

🍓 Input/Output Options:

• -i, --input FILE — the input sam file you're feeding in. [default: stdin]
• -o, --output FILE — output sam file with all your input alignments. [default: stdout]
• -d, --discordantFile FILE — dumps discordant read pairs into this file. [default: no discordant file output]
• -s, --splitterFile FILE — dumps split reads into this file, abiding by the parameters below. [default: no splitter file output]
• -u, --unmappedFile FILE — dumps unmapped/clipped reads as FASTQ into this file, abiding by the parameters below. [default: no unmapped file output]

🔥 Requires soft clipping in the input file. will output FASTQ if QUAL information is available, otherwise FASTA. iykyk.

🌈 Other Options:

• -a, --acceptDupMarks — accept the duplicate marks that are already in the input file instead of looking for duplicates in the input. trust the input, bestie.
• -e, --excludeDups — exclude reads marked as duplicates from the discordant, splitter, and/or unmapped file. bye girl 👋
• -r, --removeDups — remove duplicate reads from all output files. (this implies --excludeDups).
• --addMateTags — add MC and MQ tags to all output paired-end SAM lines. cute little tags for your mates 💖
• --ignoreUnmated — suppress abort on unmated alignments. > 🚨 Use only when you're sure the input is read-id grouped and the alignments have been filtered. do not be reckless with this one, fr fr.
• -M — run in compatibility mode; both 0x100 and 0x800 are considered chimeric. Similar to BWA MEM -M option.
• --maxSplitCount INT — maximum number of split alignments for a read to be included in the splitter file. [default: 2]
• --maxUnmappedBases INT — maximum number of un-aligned bases between two alignments to be included in the splitter file. [default: 50]
• --minIndelSize INT — minimum structural variant feature size for split alignments to be included in the splitter file. [default: 50]
• --minNonOverlap INT — minimum non-overlaping base pairs between two alignments for a read to be included in the splitter file. [default: 20]
• --minClipSize INT — minimum number of bases a mapped read must be clipped to be included in the unmapped file. [default: 20]
• -q, --quiet — output fewer statistics. sometimes you just don't wanna hear it 🤫

⭐ VERSION ⭐

0.1.24

👑 AUTHOR 👑

Greg Faust (gf4ea@virginia.edu)

and that's the whole vibe, bestie 🫶 this was samblaster: Version 0.1.24, from way back in July 2018 — go forth and mark those duplicates, you absolute main character 🧚✨💜