Pipeline for NGS data analysis ============================== The idea behind this script is have a simple way to go from raw FASTQ reads to BAM files. Briefly: 1) Read QC. % ./filter_reads.sh file_1.fastq file_2.fastq If file_2.fastq ommited assumes single end reads. 2) Read mapping. Not included here! Use your favorite read mapping program (eg. BWA, Bowtie2, SNAP, ...) 3) SNP QC % ./filter_SNP.sh run_ID $N_IND $CHR bam_list.txt $REF_SEQ $ANC_SEQ The output from this step is a BED file with the positions that passed the quality filters. This file can be used on all downstream analysis 4) Check VCF and SFS to assess overall quality of data. % Rscript analyze_vcf.R myvariants.vcf output_file Script Description ================== filter_reads.sh Script to perform raw reads QC. Namely, read filtering, quality trimming, adaptor trimming, PE read merging,... filter_SNP.sh SNP QC based on min/max depth, HWE, quality bias, strand bias, ... It calls the scripts below. get_mut_bias.pl Script to plot the mutation frequency bias along the read. It was developed to deal with ancient DNA. get_depth_thresh.R R script to automatically define the upper and lower depth coverage limits on SNPcleaner. It fits a mixture of Gamma and Neg-Binomial distribution to the empirical read coverage distribution. SNPcleaner.pl Filters sites from VCF files following a set of rules. analyze_vcf.R Script to visualize aspects of data in VCF files.