1000Bulls mapping pipeline at ABGC

<source lang='bash'>

for i in `seq 1 15`; do echo $i; python3 ABGC_mapping_v2.py -i BOV-WUR-$i -a /srv/mds01/shared/Bulls1000/F12FPCEUHK0755_alq121122/cleandata/ -r /srv/mds01/shared/Bulls1000/UMD31/umd_3_1.fa -t 12 -s cow -m bwa-aln -b 5.9 -o; done </source>

• The Python3-based masterscript
• Example of a runfile created by the master script

<source lang='bash'> java -Xmx4G -jar GenomeAnalysisTK.jar -T DepthOfCoverage -R umd_3_1.fa -I BOV-WUR-2_rh.dedup_st.reA.bam --omitDepthOutputAtEachBase --logging_level ERROR --summaryCoverageThreshold 10 --summaryCoverageThreshold 20 --summaryCoverageThreshold 30 --summaryCoverageThreshold 40 --summaryCoverageThreshold 50 --summaryCoverageThreshold 80 --summaryCoverageThreshold 90 --summaryCoverageThreshold 100 --summaryCoverageThreshold 150 --minBaseQuality 15 --minMappingQuality 30 --start 1 --stop 1000 --nBins 999 -dt NONE -o BOV-WUR-2_rh.dedup_st.reA.coverage </source>