fooliu/sapper repository overview

⁠Official Sapper docker

Sapper is a bioinformatics algorithm to call variants directly from single ChIP-seq, ATAC-seq or other similar target-enrichment genomics assay.

⁠Get Started

⁠Pull the image

docker pull fooliu/sapper

⁠Analyze your data

⁠Preprocessing

First, cd to the working directory containing ChIP-seq alignment files such as chip-seq-file.bam and control-seq-file.bam. Then

1. Clean the BAM files:

samtools view -q 30 -F 4 -F 256 -F 2048 -b chip-seq-file.bam -o chip-seq-file_clean.bam samtools view -q 30 -F 4 -F 256 -F 2048 -b control-seq-file.bam -o control-seq-file_clean.bam

1. Sort the BAM file:

samtools sort IP_clean.bam IP_clean_sorted samtools sort CTRL_clean.bam CTRL_clean_sorted

1. Peak calling (example is for paired-end data):

macs2 callpeak -f BAMPE -t IP_clean_sort.bam -c CTRL_clean_sort.bam -n MyFactor

1. Sort peak file:

sort -k1,1 -k2,2n MyFactor_peaks.narrowPeak > MyFactor_peaks.sorted.bed

1. Extract reads in peak regions:

samtools view -b IP_clean_sorted.bam -L MyFactor_peaks.sorted.bed -o IP_peaks.bam samtools view -b CTRL_clean_sorted.bam -L MyFactor_peaks.sorted.bed -o CTRL_peaks.bam

⁠Call variants from ChIP-seq data

docker run --rm -v $PWD:/data/ fooliu/sapper call -b /data/MyFactor_peaks.sorted.bed -t /data/IP_peaks.bam -c /data/CTRL_peaks.bam -o /data/MyFactor.vcf

The first part -v $PWD:/data/ will mount the CURRENT directory $PWD to /data/ in the container, so please don't forget to add /data/ to the path of input files with -b, -t, and/or -c, and don't forget to set the -o option to /data/. The final outputs will be directly written into the CURRENT directory. Extra Sapper options can be modified or added after docker run --rm -v $PWD:/data/ fooliu/sapper. The ENTRYPOINT (or the default command when running the container) has been set as macs2.

⁠Author

This Docker image is maintained and uploaded by Tao Liu [email protected]⁠.