/
genome_pipeline.sh
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/
genome_pipeline.sh
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#!/bin/bash
sample_id=$1
input_dir=./data_input
local_dir=./temp
bucket_dir=./new-berry-data/falcon
ref_dir=./ref
ref_genome=$ref_dir/human_g1k_v37.fasta
out_dir=./output
dbSNP=$ref_dir/dbsnp_138.b37.vcf
#dbSNP=$ref_dir/All_20161121.vcf.gz
#g1000_indels=$ref_dir/1000G_phase1.indels.b37.vcf
#g1000_gold_standard_indels=$ref_dir/Mills_and_1000G_gold_standard.indels.b37.vcf
start_ts=$(date +%s)
set -x
/usr/local/falcon/bin/fcs-genome align \
-r $ref_genome \
-1 ${input_dir}/${sample_id}_1.fastq.gz \
-2 ${input_dir}/${sample_id}_2.fastq.gz \
-o $local_dir/${sample_id}.bam \
-R $sample_id -S $sample_id -L $sample_id -P illumina -f
/usr/local/falcon/bin/fcs-genome bqsr \
-r $ref_genome \
-i $local_dir/${sample_id}.bam \
-o $local_dir/${sample_id}.recal.bam \
-K $dbSNP -f
/usr/local/falcon/bin/fcs-genome htc \
-r $ref_genome \
-i $local_dir/${sample_id}.recal.bam \
-O "-stand_call_conf 50" \
-O "-A RMSMappingQuality" \
-O " -maxAltAlleles 15" \
-o ${out_dir}/${sample_id}.vcf -v -f
set +x
#-O "-A BaseCounts" \
#-O "-stand_emit_conf 10.0" \
end_ts=$(date +%s)
echo "Pipeline finishes in $((end_ts - start_ts)) seconds"
#mv