This pipeline can generate regular WES, WGS, 10x WES/WGS BAMs from the corresponding FASTQ files (1 lane or 2 lanes). It was originally developed for generating the MMY 10X WGS BAMs (hg38) in Katmai.

FASTQtoBAM can run through multiple samples in a systematic way. Users can define the sample informtion, input and output paths in datamap.

There are multiple steps including trimming, mapping, sorting, merging (if two lanes), removing duplicates and indexing the BAMs.

Source code is freely available at https://github.com/ding-lab/FASTQtoBAM.git, distributed under the GNU GPLv3 license, implemented in Bash, and supported on Unix/Linux/OS X operating systems.

Run the job as nohup bash submit_FASTQtoBAM.sh 1>sample_ID.err 2>sample_ID.log &

Trimming (flexbar): barcode and adapter removal.

Read mapping (bwa & samtools): add read group information and align the reads to the reference genome (user can define the reference (hg19/hg38) in the config.sh).

Sorting (samtools): sort the intermediate BAM files.

Merging (samtools): merge the intermediate BAM files if there are two lanes from the sample (will be skipped if there is only one lane).

Removing duplicates (Picard): remove duplicates and generate the final BAM files.

Indexing (samtools): create index.

Intermediate files removal.