postdoc/indexbam.sh at master · cdbope/postdoc · GitHub

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#!/bin/bash

. /mnt/lustre/groups/CBBI0818/Team_Sim/config.txt

#ANC=
#ANC=$1

ID=AFR${ANC}

#echo -e "@RG\tID:ga\tSM:${ID}\tLB:ga\tPL:Illumina" > ${bam}rg.${ANC}.txt
#${samtools} view -h ${BAM}AFR/High/AFR_26_sim_reads_high_golden.bam | cat ${bam}rg.${ANC}.txt - | awk '{ if (substr($1,1,1)=="@") print; else printf "%s\tRG:Z:ga\n",$0; }' | ${samtools} view -uS - | ${samtools} rmdup - - | ${samtools} rmdup -s - ${bam}AFR_${ANC}_sim_highcov_golden.fixed.bam

#${samtools} index ${bam}AFR_${ANC}_sim_highcov_golden.fixed.bam

#${samtools} calmd -Erb ${bam}AFR_${ANC}_sim_highcov_golden.fixed.bam ${REF}ucsc.hg19.fasta > ${bam}AFR_${ANC}_sim_highcov_golden.calmd.bam1
#${samtools} index ${bam}AFR_${ANC}_sim_highcov_golden.calmd.bam

${samtool} view -H ${BAM}AFR/High/AFR_${ANC}_sim_reads_high_golden.bam | \
sed 's,ID:NEAT,ID:sample_${ANC}\tSM:${ID}\tLB:477\tPL:Illumina,g' | \
${samtool} reheader - \
${BAM}AFR/High/AFR_${ANC}_sim_reads_high_golden.bam > ${BAM}AFR/High/AFR_${ANC}_sim_reads_high_golden.fixed.bam

${samtool} index ${BAM}AFR/High/AFR_${ANC}_sim_reads_high_golden.fixed.bam

#${EXE_JAVA} -Xmx2g -XX:ParallelGCThreads=1 -Djava.io.tmpdir=${tmp} -jar ${picard}AddOrReplaceReadGroups.jar \
#I=${BAM}AFR/High/AFR_${ANC}_sim_reads_high_golden.bam \
#OUTPUT=${wkd}AFR_${ANC}_sim_highcov_golden.fixed.bam \
#ID=sample${ANC} LB=FCC007KABXX PU=GTCAATTT PL=illumina SM=${ID}

${samtool} calmd -Erb ${BAM}AFR/High/AFR_${ANC}_sim_reads_high_golden.fixed.bam \
${REF}ucsc.hg19.fasta > ${BAM}AFR/High/AFR_${ANC}_sim_reads_high_golden.calmd.bam
${samtool} index ${BAM}AFR/High/AFR_${ANC}_sim_reads_high_golden.calmd.bam


#${EXE_JAVA} -Xmx2g -XX:ParallelGCThreads=1 -Djava.io.tmpdir=${tmp} -jar ${picard}BuildBamIndex.jar \
#$INPUT=${bam}