impute/RUN at master · Chris1221/impute · GitHub

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#!/bin/bash

################# !!! #####################
#                                         #
#         THESE ARE LOCALLY RUN           #
#         bash run; cnt+z; disown         #
#                                         #
################  !!! #####################

#source the config parms

source CONFIG

# first split the chromosomes up, note that this script is modified to
# omit the exlude snps, because we only generate those after
# the align check step.

cd $DD
#remove dups, maybe make this first?
Rscript ${R}app/remove_dup.R $DD $DATA


for CHR in $(seq 1 22)
do

	#local split by
	$plink --noweb --bfile $DATA --chr $CHR --exclude exclude_snp_list.txt --make-bed --out ${DATA}_chr${CHR}

	#align check 1
	${shapeit} -check -B ${DATA}_chr${CHR} -M ${RD}genetic_map_chr${CHR}_combined_b37.txt --input-ref ${RD}ALL.chr${CHR}.integrated_phase1_v3.20101123.snps_indels_svs.genotypes.nomono.haplotypes.gz ${RD}ALL.chr${CHR}.integrated_phase1_v3.20101123.snps_indels_svs.genotypes.nomono.legend.gz ${RD}ALL.integrated_phase1_v3.20101123.snps_indels_svs.genotypes.sample --output-log ${DATA}_alignment_chr${CHR}

	#cleanup
	#rm -f neam_alignment_chr*.log
	#rm -f KIS3_AA_QC_complete_150731_chr*.*

	# grab bad snps


	cat ${DATA}_alignment_chr${CHR}.snp.strand | grep "Strand" | awk '{ print $3 }' > flip.chr${CHR}.txt

	cat ${DATA}_alignment_chr${CHR}.snp.strand | grep "Missing" | awk '{ print $3 }' > exclude.chr${CHR}.txt

	#flip these in the data

	$plink --noweb --bfile ${DATA}_chr${CHR} --flip flip.chr${CHR}.txt --make-bed --out ${DATA}_chr${CHR}.flipped

	#check again and pipe all problems to an exclude

	${shapeit} -check -B ${DATA}_chr${CHR}.flipped -M ${RD}genetic_map_chr${CHR}_combined_b37.txt --input-ref ${RD}ALL.chr${CHR}.integrated_phase1_v3.20101123.snps_indels_svs.genotypes.nomono.haplotypes.gz ${RD}ALL.chr${CHR}.integrated_phase1_v3.20101123.snps_indels_svs.genotypes.nomono.legend.gz ${RD}ALL.integrated_phase1_v3.20101123.snps_indels_svs.genotypes.sample --output-log ${DATA}_alignment_chr${CHR}.flipped

	cat ${DATA}_alignment_chr${CHR}.flipped.snp.strand | grep "Strand" | awk '{ print $3 }' >> exclude.chr${CHR}.txt
	cat ${DATA}_alignment_chr${CHR}.flipped.snp.strand | grep "Missing" | awk '{ print $3 }' >> exclude.chr${CHR}.txt

	#prephasing

	qsub -N ${DATA}_chr${CHR}_prephase -V ${R}app/new_prephase.sh $CHR

done