Tools to process LIANTI sequence data
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data added auxiliary data May 21, 2016
.gitignore makefile May 4, 2016
Makefile add CV plot to assess uniformity Jul 11, 2016
README.md
bedidx.c r83: Lorenz curve May 27, 2016
bgzf.c start to work on allele grouping May 4, 2016
bgzf.h start to work on allele grouping May 4, 2016
cnv.c r68: harder to call 1-copy losses May 22, 2016
count.c r53: a bit better CLI help May 16, 2016
cv.c allow cv to take a BED file (for example, output of lianti count) as … Jul 12, 2016
faidx.c prepare to port htsbox pileup May 22, 2016
faidx.h
group.c r112: bugfix: first mapq not counted Aug 14, 2016
hts.c backup May 18, 2016
hts.h start to work on allele grouping May 4, 2016
kdq.h start to work on allele grouping May 4, 2016
khash.h first commit Apr 27, 2016
kseq.h first commit Apr 27, 2016
ksort.h r55: backup May 19, 2016
kstring.h start to work on allele grouping May 4, 2016
kthread.c r116: updated kthread; option to change maxcnt Mar 16, 2017
kvec.h first commit Apr 27, 2016
ldup.c
lorenz.c r85: fixed an integer overflow May 28, 2016
main.c r142: %.2g => %.1f Aug 2, 2018
pileup.c r142: %.2g => %.1f Aug 2, 2018
plp-diff.js density filter not working Jul 2, 2018
plp-joint.js r158: fixed JV Feb 17, 2019
razf.c prepare to port htsbox pileup May 22, 2016
razf.h prepare to port htsbox pileup May 22, 2016
sam.c
sam.h start to work on allele grouping May 4, 2016
sv.c r103: changed the default sv thresholds Jun 21, 2016
trim.c r105: fixed a typo in quality merging Jun 22, 2016

README.md

Getting Started

git clone https://github.com/lh3/lianti
cd lianti && make
# preprocessing, mapping and marking duplicates
seqtk mergepe read1.fq.gz read2.fq.gz | ./lianti trim - | bwa mem -Cpt8 ref.fa - \
  | samtools view -uS - | sambamba sort /dev/stdin -o /dev/stdout | ./lianti ldup - > aln.bam
# calling SNVs
./lianti pileup -ycf ref.fa -P20 -L1 bulk.bam lianti.bam > raw.vcf
k8 plp-diff.js raw.vcf > filtered.txt

Introduction

LIANTI is a single-cell whole-genome amplification method. This repo implements tools to preprocess raw LIANTI sequence data and to call sequence variations from the alignment. Probably you would like to use the trim command to trim adapters, identify barcodes and merge overlapping read ends. It is non-trivial to reimplement these tedious functionality on your own. ldup marks PCR duplicates in a barcode-aware manner. It has been superseded by the ldup command in the adna repo which is more general. You may consider to call SNVs with this toolkit, too, but it is not that hard to roll your own anyway. Calling SVs and CNVs is hard with any callers. This repo does consider some LIANTI-specific features, but generally you should not expect it to be the state of art. Good luck.