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subset-bam.sh
executable file
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subset-bam.sh
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#!/usr/bin/env bash
set -ex
FASTA=../data/human_g1k_v37.fa.gz
FASTQ_PREFIX=../generating-reads/HG00119-reads
BAMIN=../alignment-accuracy/HG00119-bwa.bam
DO_NOT_INDEX=${1}
# Starting this script with the argument --do-not-index will skip the
# BAM file indexing. Due to some bug in pysam the index invocation does
# not work on Linux
BAMOUT=HG00119-bwa-snps.bam
mitty -v4 debug subset-bam \
${BAMIN} \
${FASTQ_PREFIX}-corrupt-lq.txt \
${BAMOUT} \
--v-range 0 0 \
--reject-reference-reads \
--processes 2 ${DO_NOT_INDEX}
BAMOUT=HG00119-bwa-good-del.bam
mitty -v4 debug subset-bam \
${BAMIN} \
${FASTQ_PREFIX}-corrupt-lq.txt \
${BAMOUT} \
--v-range -10000 -1 \
--d-range -5 5 \
--reject-reference-reads \
--processes 2 ${DO_NOT_INDEX}
BAMOUT=HG00119-bwa-poor-del.bam
mitty -v4 debug subset-bam \
${BAMIN} \
${FASTQ_PREFIX}-corrupt-lq.txt \
${BAMOUT} \
--v-range -10000 -1 \
--d-range -5 5 \
--reject-d-range \
--reject-reference-reads \
--processes 2 ${DO_NOT_INDEX}