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gen-reads.sh
executable file
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gen-reads.sh
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#!/usr/bin/env bash
set -ex
FASTA=../data/human_g1k_v37.fa.gz
SAMPLEVCF=../data/1kg.20.22.vcf.gz
SAMPLENAME=HG00119
REGION_BED=region.bed
FILTVCF=HG00119-filt.vcf.gz
READMODEL=1kg-pcr-free.pkl
COVERAGE=30
READ_GEN_SEED=7
FASTQ_PREFIX=HG00119-reads
READ_CORRUPT_SEED=8
mitty -v4 filter-variants \
${SAMPLEVCF} \
${SAMPLENAME} \
${REGION_BED} \
- \
2> vcf-filter.log | bgzip -c > ${FILTVCF}
tabix -p vcf ${FILTVCF}
mitty -v4 generate-reads \
${FASTA} \
${FILTVCF} \
${SAMPLENAME} \
${REGION_BED} \
${READMODEL} \
${COVERAGE} \
${READ_GEN_SEED} \
>(gzip > ${FASTQ_PREFIX}1.fq.gz) \
${FASTQ_PREFIX}-lq.txt \
--fastq2 >(gzip > ${FASTQ_PREFIX}2.fq.gz) \
--threads 2
mitty utils qname-stats \
${FASTQ_PREFIX}1.fq.gz \
${FASTQ_PREFIX}-lq.txt
mitty -v4 corrupt-reads \
${READMODEL} \
${FASTQ_PREFIX}1.fq.gz >(gzip > ${FASTQ_PREFIX}-corrupt1.fq.gz) \
${FASTQ_PREFIX}-lq.txt \
${FASTQ_PREFIX}-corrupt-lq.txt \
${READ_CORRUPT_SEED} \
--fastq2-in ${FASTQ_PREFIX}2.fq.gz \
--fastq2-out >(gzip > ${FASTQ_PREFIX}-corrupt2.fq.gz) \
--threads 2
mitty utils qname-stats \
${FASTQ_PREFIX}-corrupt1.fq.gz \
${FASTQ_PREFIX}-corrupt-lq.txt