SCCNV: a software tool for identifying copy number variation from single-cell whole-genome sequencing
Version 1.0
Updated date: 2018.07.27
Author: Xiao Dong
Email: [email protected], [email protected]
Licensed under the GNU Affero General Public License version 3 or later
python 2 or python 3
python modules os, argparse, math, numpy
bedtools
Below is an example for cell_A. I recommend filter out reads with mapq<30.
samtools view -b -q 30 ./bam/cell_A.bam > ./bam_mapq30/cell_A.mapq30.bam
samtools index ./bam_mapq30/cell_A.mapq30.bam
Provide a file (e.g. “bamlist.txt”) with the following content,
./bam_mapq30/cell_A.mapq30.bam
./bam_mapq30/cell_B.mapq30.bam
./bam_mapq30/cell_C.mapq30.bam
python sccnv.py -i bamlist.txt -o cellsAtoC -k False -r True
One can prepare bed files for calculation using bedtools and samtools (for every cell in paralleles),
mkdir cellsAtoC
bedtools makewindows -g ./resource/hg19.chrlength.txt -w 500000 > ./cellsAtoC/hg19.bin500000.bed
samtools bedcov ./cellsAtoC/hg19.bin500000.bed ../bam_mapq30/cell_A.mapq30.bam > ./cellsAtoC/cell_A.depth.bin500000.bed
And skip the related step in SCCNV,
python sccnv.py -i bamlist.txt -o cellsAtoC -k True -r True
v1.0 2018.07.26, release version.
v0.0.3 2018.07.25, rewrote in Python.
v0.0.2 2017.08, fixed bugs.
v0.0.1 2016.09, drafted script in R.