Arabidposis-mutants-pipeline

Mapping and attribute statistics

1.fastqc.sh

Shell script of fastqc process to evaluate fastq file sequence quality

2.mapping.sh

Shell script to align sequence file to TAIR10 reference

3.attribute-stats.sh

Shell script to evaluate bam files' attributes like depth,coverage,etc

Detect-mutation

1.call-variants.sh

Shell script to call mutation sites using GATK

2.detect_mutation.sh

Shell script to screen out candidate snv and indel(insertion and deletion) sites

Simulation

1.simulation.sh

Shell script to simulate mutation detect pipeline to evaluate this method's FNR and callable sites ratio

2.sim_mutation_reads.pl

Perl script to simulate reads with synthetic mutations use the method describled in Keightley et al.