03b_summary_variant_calling_batch2.sh

#!/bin/bash
#####################################
# Alexandra Jansen van Rensburg
# Last modified 23/10/2018 15:27:00
####################################

# Script to summarise variant calls in bcf files as generated by 03a_variant_calling_bluecp3.sh
# outputs a raw combined variant file (.bcf) and a filtered file (.bcf) in the input folder. 
# Runs in a few minutes in the home directory (don't need to submit to Blue Crystal). 
# Estimated time: 2 minutes for 59 pheasant samples mapped to Gallus gallus genome. 


##Specify resources
#PBS -N 03b_G1.FINALTEST  ##job name
#PBS -l nodes=1:ppn=1  #nr of nodes and processors per node
#PBS -l mem=16gb #RAM
#PBS -l walltime=3:00:00 ##wall time.  
#PBS -j oe  #concatenates error and output files (with prefix job1)


module load apps/bcftools-1.8

##Work in current directory
cd $PBS_O_WORKDIR 

bcftools concat -O b -a -d none -f 03_variants.FINALTESTS/bcflist.batch2 --threads 1  > 03_variants.FINALTESTS/OUTF.b.batch02.bcf
bcftools index 03_variants.FINALTESTS/OUTF.b.batch02.bcf


#/newhome/aj18951/bristol-velocity/AJvR_VelocityPipeline/wrapper/03b_call_SNVs_summarize_bluecp3_v2.sh \
#-i /newhome/aj18951/G1_Thymelicus_acteon/03_variants.FINALTESTS -n 1;
# -flt -scov 0.4 -qs 20 -mindp 10 -maxdp 4000 -noindel -nomulti -nopriv;