Short read mapping pipeline pig

The latest short-read mapping pipeline for the pig project is based on a Python3 script that creates a shell script that can subsequently be executed from the command line or submitted to the cluster using SLURM. The latest version of the Python3 script can be found at GitHub.

Prerequisites

• bwa 5.9 /cm/shared/apps/WUR/ABGC/bwa/bwa-0.5.9/
• bwa 7.5 /cm/shared/apps/WUR/ABGC/bwa/bwa-0.7.5a/
• samtools 1.19 /cm/shared/apps/WUR/ABGC/samtools/samtools-0.1.19/
• samtools 1.12 /cm/shared/apps/WUR/ABGC/samtools/samtools-0.1.12a/
• picard /cm/shared/apps/WUR/ABGC/picard/picard-tools-1.93/
• GATK /cm/shared/apps/WUR/ABGC/GATK/GATK2.6/
• Mosaik /path/to/mosaik/ref.dat
• Mosaik Jump Library /path/to/mosaikjump/ref.j15
• dbSNPfile=reffolder+'/dbSNP/dbSNP.vcf'
• gatk_gvcf /cm/shared/apps/WUR/ABGC/GATK/GATK_gVCFmod/
• gvcftools /cm/shared/apps/WUR/ABGC/gvcftools/gvcftools-0.16/bin/
• helper scripts /cm/shared/apps/WUR/ABGC/abgsascripts/
• path to sqlite db path (for cow) /path/to/sqlite/Bulls1000/
• Variant Effect Predictor (VEP) /cm/shared/apps/WUR/ABGC/variant_effect_predictor/VEP231213/

Basic execution

<source lang='bash'> (virtenv)[megen002@nfs01 rundir]$ python ABGC_mapping_v2.py -i LW22F04 -a /lustre/nobackup/WUR/ABGC/shared/Pig/ABGSA/ -r /lustre/nobackup/WUR/ABGC/shared/Pig/Sscrofa_build10_2/Ensembl72/Sus_scrofa.Sscrofa10.2.72.dna.toplevel.fa -t 4 </source> The code should produce the following shell script, ready for execution with SLURM.

Automated runfile creation

<source lang='bash'> mysql -u ABGSAuser -h scomp1095.wurnet.nl -p ABGSAschema -e 'select ABG_individual_id from ABGSAschema_main where archive_name like "ABGSA0%" group by ABG_individual_id' >list.txt FILES=`cat list.txt` for ID in $FILES; do python ABGC_mapping_v2.py -i $ID -a /lustre/nobackup/WUR/ABGC/shared/Pig/ABGSA/ -r /lustre/nobackup/WUR/ABGC/shared/Pig/Sscrofa_build10_2/Ensembl72/Sus_scrofa.Sscrofa10.2.72.dna.toplevel.fa -t 4; done </source>

See also

Animal Breeding & Genomics Sequence Archives